HEADER LIGASE/ANTIBIOTIC 03-NOV-15 5EKD
TITLE HUMAN MITOCHONDRIAL TRYPTOPHANYL-TRNA SYNTHETASE BOUND BY INDOLMYCIN
TITLE 2 AND MN*ATP.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRYPTOPHAN--TRNA LIGASE, MITOCHONDRIAL;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: (MT)TRPRS,TRYPTOPHANYL-TRNA SYNTHETASE,TRPRS;
COMPND 5 EC: 6.1.1.2;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: WARS2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28
KEYWDS TRPRS, INDOLMYCIN, MITOCHONDRIAL, COMPLEX, LIGASE-ANTIBIOTIC COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.L.WILLIAMS,C.W.CARTER JR.
REVDAT 5 27-SEP-23 5EKD 1 HETSYN LINK
REVDAT 4 25-DEC-19 5EKD 1 REMARK
REVDAT 3 20-SEP-17 5EKD 1 REMARK
REVDAT 2 07-DEC-16 5EKD 1 AUTHOR
REVDAT 1 16-NOV-16 5EKD 0
JRNL AUTH T.L.WILLIAMS,C.W.CARTER JR.
JRNL TITL BINDING OF MG2+ATP ENHANCES INHIBITION OF HUMAN
JRNL TITL 2 MITOCHONDRIAL TRYPTOPHANYL-TRNA SYNTHETASE BY INDOLMYCIN
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.82 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.8_1069
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.06
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 3 NUMBER OF REFLECTIONS : 60550
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.172
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : 0.207
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070
REMARK 3 FREE R VALUE TEST SET COUNT : 3070
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 29.0651 - 5.0903 0.96 2653 130 0.1660 0.1972
REMARK 3 2 5.0903 - 4.0438 0.98 2636 125 0.1344 0.1493
REMARK 3 3 4.0438 - 3.5336 0.98 2623 154 0.1391 0.1671
REMARK 3 4 3.5336 - 3.2110 0.99 2614 157 0.1561 0.1862
REMARK 3 5 3.2110 - 2.9811 0.99 2654 142 0.1582 0.1935
REMARK 3 6 2.9811 - 2.8055 0.99 2593 161 0.1682 0.2191
REMARK 3 7 2.8055 - 2.6651 0.99 2634 142 0.1651 0.2059
REMARK 3 8 2.6651 - 2.5491 0.99 2621 141 0.1662 0.2312
REMARK 3 9 2.5491 - 2.4511 0.99 2605 141 0.1633 0.2118
REMARK 3 10 2.4511 - 2.3665 0.99 2644 148 0.1656 0.2209
REMARK 3 11 2.3665 - 2.2926 0.99 2640 131 0.1672 0.2052
REMARK 3 12 2.2926 - 2.2271 0.99 2580 143 0.1728 0.2279
REMARK 3 13 2.2271 - 2.1684 0.99 2672 144 0.1790 0.2381
REMARK 3 14 2.1684 - 2.1156 0.99 2613 132 0.1853 0.2113
REMARK 3 15 2.1156 - 2.0675 0.99 2672 141 0.1925 0.2187
REMARK 3 16 2.0675 - 2.0235 0.99 2590 133 0.1984 0.2356
REMARK 3 17 2.0235 - 1.9830 0.99 2645 138 0.2117 0.2587
REMARK 3 18 1.9830 - 1.9456 0.99 2560 141 0.2221 0.2782
REMARK 3 19 1.9456 - 1.9109 0.99 2676 142 0.2457 0.3025
REMARK 3 20 1.9109 - 1.8785 0.99 2553 139 0.2615 0.3048
REMARK 3 21 1.8785 - 1.8482 0.99 2720 131 0.2651 0.2926
REMARK 3 22 1.8482 - 1.8198 0.88 2282 114 0.2834 0.3231
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.700
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.004 5380
REMARK 3 ANGLE : 0.912 7314
REMARK 3 CHIRALITY : 0.047 849
REMARK 3 PLANARITY : 0.004 905
REMARK 3 DIHEDRAL : 17.382 2050
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5EKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-15.
REMARK 100 THE DEPOSITION ID IS D_1000215044.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-OCT-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60563
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820
REMARK 200 RESOLUTION RANGE LOW (A) : 29.060
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 2.300
REMARK 200 R MERGE (I) : 0.07700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1
REMARK 200 DATA REDUNDANCY IN SHELL : 2.30
REMARK 200 R MERGE FOR SHELL (I) : 0.59400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: 5DK4
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.26
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, GLYCEROL, PEG 5000,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.14450
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.04350
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.14450
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.04350
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 26330 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 MN MN A 404 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 755 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 778 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B 703 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B 739 LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 ALA A 18
REMARK 465 LEU A 19
REMARK 465 HIS A 20
REMARK 465 LYS A 21
REMARK 465 GLY A 22
REMARK 465 SER A 23
REMARK 465 ALA A 24
REMARK 465 ALA A 25
REMARK 465 ALA A 26
REMARK 465 PRO A 27
REMARK 465 ALA A 28
REMARK 465 LEU A 29
REMARK 465 GLN A 30
REMARK 465 LYS A 31
REMARK 465 ASP A 32
REMARK 465 SER A 33
REMARK 465 ALA B 18
REMARK 465 LEU B 19
REMARK 465 HIS B 20
REMARK 465 LYS B 21
REMARK 465 GLY B 22
REMARK 465 SER B 23
REMARK 465 ALA B 24
REMARK 465 ALA B 25
REMARK 465 ALA B 26
REMARK 465 PRO B 27
REMARK 465 ALA B 28
REMARK 465 LYS B 148
REMARK 465 GLN B 149
REMARK 465 LYS B 150
REMARK 465 HIS B 151
REMARK 465 ASP B 152
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 CD LYS B 145 O HOH B 536 1.03
REMARK 500 HD2 LYS B 145 O HOH B 536 1.13
REMARK 500 CE LYS B 145 O HOH B 536 1.23
REMARK 500 HD3 LYS B 145 O HOH B 536 1.30
REMARK 500 HE3 LYS B 145 O HOH B 536 1.31
REMARK 500 HE2 MET B 130 O HOH B 526 1.54
REMARK 500 O VAL B 255 HG23 THR B 256 1.55
REMARK 500 OE1 GLN B 249 HH11 ARG B 252 1.55
REMARK 500 HH11 ARG B 61 OE2 GLU B 65 1.57
REMARK 500 CE MET B 130 O HOH B 526 1.86
REMARK 500 OE1 GLN B 249 NH1 ARG B 252 1.88
REMARK 500 O HOH B 707 O HOH B 754 2.12
REMARK 500 O HOH A 667 O HOH A 682 2.12
REMARK 500 O HOH B 639 O HOH B 680 2.12
REMARK 500 NH1 ARG B 61 OE2 GLU B 65 2.14
REMARK 500 O HOH A 515 O HOH A 718 2.14
REMARK 500 O HOH B 706 O HOH B 734 2.16
REMARK 500 O HOH A 737 O HOH A 777 2.17
REMARK 500 O HOH A 741 O HOH A 758 2.17
REMARK 500 O HOH A 563 O HOH A 749 2.18
REMARK 500 O HOH B 531 O HOH B 679 2.18
REMARK 500 O HOH A 748 O HOH A 781 2.19
REMARK 500 O HOH A 783 O HOH B 748 2.19
REMARK 500 O HOH A 648 O HOH A 734 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 HH11 ARG A 135 HG SER B 33 3455 1.21
REMARK 500 O HOH A 736 O HOH B 701 3455 2.14
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 HIS A 77 NE2 HIS A 77 CD2 -0.074
REMARK 500 HIS A 138 NE2 HIS A 138 CD2 -0.067
REMARK 500 HIS A 185 NE2 HIS A 185 CD2 -0.075
REMARK 500 GLU A 312 CD GLU A 312 OE1 -0.070
REMARK 500 HIS A 330 NE2 HIS A 330 CD2 -0.066
REMARK 500 HIS B 77 NE2 HIS B 77 CD2 -0.083
REMARK 500 ARG B 89 CA ARG B 89 C 0.188
REMARK 500 ARG B 89 CA ARG B 89 C 0.185
REMARK 500 HIS B 140 NE2 HIS B 140 CD2 -0.067
REMARK 500 HIS B 175 NE2 HIS B 175 CD2 -0.077
REMARK 500 HIS B 185 NE2 HIS B 185 CD2 -0.083
REMARK 500 HIS B 330 NE2 HIS B 330 CD2 -0.081
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ALA A 55 -51.79 -138.63
REMARK 500 PHE A 203 -50.08 -125.56
REMARK 500 MET A 214 42.22 -94.23
REMARK 500 THR A 256 -125.86 -127.66
REMARK 500 ASP A 265 80.89 -155.68
REMARK 500 ALA B 55 -58.92 -136.64
REMARK 500 MET B 214 42.81 -96.18
REMARK 500 ASP B 265 86.26 -154.65
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 783 DISTANCE = 6.06 ANGSTROMS
REMARK 525 HOH B 758 DISTANCE = 5.92 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 404 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 312 OE1
REMARK 620 2 GLU A 312 OE1 0.0
REMARK 620 3 HOH A 533 O 88.0 88.0
REMARK 620 4 HOH A 533 O 90.7 90.7 176.6
REMARK 620 5 HOH A 703 O 89.4 89.4 93.6 89.6
REMARK 620 6 HOH A 703 O 171.8 171.8 88.1 92.8 98.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 403 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ATP A 402 O3G
REMARK 620 2 ATP A 402 O2B 85.2
REMARK 620 3 ATP A 402 O2A 86.1 87.7
REMARK 620 4 HOH A 529 O 170.6 91.3 85.0
REMARK 620 5 HOH A 555 O 90.8 175.9 91.8 92.6
REMARK 620 6 HOH A 691 O 96.5 90.5 176.7 92.3 90.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN B 404 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU B 312 OE1
REMARK 620 2 GLU B 312 OE1 0.0
REMARK 620 3 HOH B 511 O 90.1 90.1
REMARK 620 4 HOH B 511 O 84.6 84.6 166.2
REMARK 620 5 HOH B 705 O 101.6 101.6 98.1 95.4
REMARK 620 6 HOH B 705 O 159.3 159.3 92.8 87.9 98.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN B 403 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ATP B 402 O1G
REMARK 620 2 ATP B 402 O1B 82.9
REMARK 620 3 ATP B 402 O2A 89.6 86.4
REMARK 620 4 HOH B 522 O 172.8 95.7 83.3
REMARK 620 5 HOH B 618 O 87.0 169.7 91.9 94.1
REMARK 620 6 HOH B 678 O 95.3 90.5 173.9 91.7 92.0
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5BX A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5BX B 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ATP B 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 406
DBREF 5EKD A 18 360 UNP Q9UGM6 SYWM_HUMAN 18 360
DBREF 5EKD B 18 360 UNP Q9UGM6 SYWM_HUMAN 18 360
SEQRES 1 A 343 ALA LEU HIS LYS GLY SER ALA ALA ALA PRO ALA LEU GLN
SEQRES 2 A 343 LYS ASP SER LYS LYS ARG VAL PHE SER GLY ILE GLN PRO
SEQRES 3 A 343 THR GLY ILE LEU HIS LEU GLY ASN TYR LEU GLY ALA ILE
SEQRES 4 A 343 GLU SER TRP VAL ARG LEU GLN ASP GLU TYR ASP SER VAL
SEQRES 5 A 343 LEU TYR SER ILE VAL ASP LEU HIS SER ILE THR VAL PRO
SEQRES 6 A 343 GLN ASP PRO ALA VAL LEU ARG GLN SER ILE LEU ASP MET
SEQRES 7 A 343 THR ALA VAL LEU LEU ALA CYS GLY ILE ASN PRO GLU LYS
SEQRES 8 A 343 SER ILE LEU PHE GLN GLN SER GLN VAL SER GLU HIS THR
SEQRES 9 A 343 GLN LEU SER TRP ILE LEU SER CYS MET VAL ARG LEU PRO
SEQRES 10 A 343 ARG LEU GLN HIS LEU HIS GLN TRP LYS ALA LYS THR THR
SEQRES 11 A 343 LYS GLN LYS HIS ASP GLY THR VAL GLY LEU LEU THR TYR
SEQRES 12 A 343 PRO VAL LEU GLN ALA ALA ASP ILE LEU LEU TYR LYS SER
SEQRES 13 A 343 THR HIS VAL PRO VAL GLY GLU ASP GLN VAL GLN HIS MET
SEQRES 14 A 343 GLU LEU VAL GLN ASP LEU ALA GLN GLY PHE ASN LYS LYS
SEQRES 15 A 343 TYR GLY GLU PHE PHE PRO VAL PRO GLU SER ILE LEU THR
SEQRES 16 A 343 SER MET LYS LYS VAL LYS SER LEU ARG ASP PRO SER ALA
SEQRES 17 A 343 LYS MET SER LYS SER ASP PRO ASP LYS LEU ALA THR VAL
SEQRES 18 A 343 ARG ILE THR ASP SER PRO GLU GLU ILE VAL GLN LYS PHE
SEQRES 19 A 343 ARG LYS ALA VAL THR ASP PHE THR SER GLU VAL THR TYR
SEQRES 20 A 343 ASP PRO ALA GLY ARG ALA GLY VAL SER ASN ILE VAL ALA
SEQRES 21 A 343 VAL HIS ALA ALA VAL THR GLY LEU SER VAL GLU GLU VAL
SEQRES 22 A 343 VAL ARG ARG SER ALA GLY MET ASN THR ALA ARG TYR LYS
SEQRES 23 A 343 LEU ALA VAL ALA ASP ALA VAL ILE GLU LYS PHE ALA PRO
SEQRES 24 A 343 ILE LYS ARG GLU ILE GLU LYS LEU LYS LEU ASP LYS ASP
SEQRES 25 A 343 HIS LEU GLU LYS VAL LEU GLN ILE GLY SER ALA LYS ALA
SEQRES 26 A 343 LYS GLU LEU ALA TYR THR VAL CYS GLN GLU VAL LYS LYS
SEQRES 27 A 343 LEU VAL GLY PHE LEU
SEQRES 1 B 343 ALA LEU HIS LYS GLY SER ALA ALA ALA PRO ALA LEU GLN
SEQRES 2 B 343 LYS ASP SER LYS LYS ARG VAL PHE SER GLY ILE GLN PRO
SEQRES 3 B 343 THR GLY ILE LEU HIS LEU GLY ASN TYR LEU GLY ALA ILE
SEQRES 4 B 343 GLU SER TRP VAL ARG LEU GLN ASP GLU TYR ASP SER VAL
SEQRES 5 B 343 LEU TYR SER ILE VAL ASP LEU HIS SER ILE THR VAL PRO
SEQRES 6 B 343 GLN ASP PRO ALA VAL LEU ARG GLN SER ILE LEU ASP MET
SEQRES 7 B 343 THR ALA VAL LEU LEU ALA CYS GLY ILE ASN PRO GLU LYS
SEQRES 8 B 343 SER ILE LEU PHE GLN GLN SER GLN VAL SER GLU HIS THR
SEQRES 9 B 343 GLN LEU SER TRP ILE LEU SER CYS MET VAL ARG LEU PRO
SEQRES 10 B 343 ARG LEU GLN HIS LEU HIS GLN TRP LYS ALA LYS THR THR
SEQRES 11 B 343 LYS GLN LYS HIS ASP GLY THR VAL GLY LEU LEU THR TYR
SEQRES 12 B 343 PRO VAL LEU GLN ALA ALA ASP ILE LEU LEU TYR LYS SER
SEQRES 13 B 343 THR HIS VAL PRO VAL GLY GLU ASP GLN VAL GLN HIS MET
SEQRES 14 B 343 GLU LEU VAL GLN ASP LEU ALA GLN GLY PHE ASN LYS LYS
SEQRES 15 B 343 TYR GLY GLU PHE PHE PRO VAL PRO GLU SER ILE LEU THR
SEQRES 16 B 343 SER MET LYS LYS VAL LYS SER LEU ARG ASP PRO SER ALA
SEQRES 17 B 343 LYS MET SER LYS SER ASP PRO ASP LYS LEU ALA THR VAL
SEQRES 18 B 343 ARG ILE THR ASP SER PRO GLU GLU ILE VAL GLN LYS PHE
SEQRES 19 B 343 ARG LYS ALA VAL THR ASP PHE THR SER GLU VAL THR TYR
SEQRES 20 B 343 ASP PRO ALA GLY ARG ALA GLY VAL SER ASN ILE VAL ALA
SEQRES 21 B 343 VAL HIS ALA ALA VAL THR GLY LEU SER VAL GLU GLU VAL
SEQRES 22 B 343 VAL ARG ARG SER ALA GLY MET ASN THR ALA ARG TYR LYS
SEQRES 23 B 343 LEU ALA VAL ALA ASP ALA VAL ILE GLU LYS PHE ALA PRO
SEQRES 24 B 343 ILE LYS ARG GLU ILE GLU LYS LEU LYS LEU ASP LYS ASP
SEQRES 25 B 343 HIS LEU GLU LYS VAL LEU GLN ILE GLY SER ALA LYS ALA
SEQRES 26 B 343 LYS GLU LEU ALA TYR THR VAL CYS GLN GLU VAL LYS LYS
SEQRES 27 B 343 LEU VAL GLY PHE LEU
HET 5BX A 401 19
HET ATP A 402 43
HET MN A 403 1
HET MN A 404 1
HET 5BX B 401 19
HET ATP B 402 43
HET MN B 403 1
HET MN B 404 1
HET GOL B 405 14
HET GOL B 406 14
HETNAM 5BX (5S)-5-[(1R)-1-(1H-INDOL-3-YL)ETHYL]-2-(METHYLAMINO)-1,
HETNAM 2 5BX 3-OXAZOL-4(5H)-ONE
HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
HETNAM MN MANGANESE (II) ION
HETNAM GOL GLYCEROL
HETSYN 5BX INDOLEMYCIN; INDOLMYCIN
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 5BX 2(C14 H15 N3 O2)
FORMUL 4 ATP 2(C10 H16 N5 O13 P3)
FORMUL 5 MN 4(MN 2+)
FORMUL 11 GOL 2(C3 H8 O3)
FORMUL 13 HOH *541(H2 O)
HELIX 1 AA1 HIS A 48 ALA A 55 1 8
HELIX 2 AA2 ALA A 55 TYR A 66 1 12
HELIX 3 AA3 VAL A 74 ILE A 79 1 6
HELIX 4 AA4 ASP A 84 GLY A 103 1 20
HELIX 5 AA5 SER A 115 VAL A 117 5 3
HELIX 6 AA6 SER A 118 CYS A 129 1 12
HELIX 7 AA7 ARG A 132 HIS A 138 1 7
HELIX 8 AA8 LEU A 139 ALA A 144 1 6
HELIX 9 AA9 THR A 146 GLY A 153 1 8
HELIX 10 AB1 THR A 154 LEU A 170 1 17
HELIX 11 AB2 GLY A 179 ASP A 181 5 3
HELIX 12 AB3 GLN A 182 GLY A 201 1 20
HELIX 13 AB4 ASP A 233 THR A 237 5 5
HELIX 14 AB5 SER A 243 ALA A 254 1 12
HELIX 15 AB6 ARG A 269 GLY A 284 1 16
HELIX 16 AB7 SER A 286 SER A 294 1 9
HELIX 17 AB8 ASN A 298 LYS A 325 1 28
HELIX 18 AB9 ASP A 327 GLY A 358 1 32
HELIX 19 AC1 HIS B 48 ALA B 55 1 8
HELIX 20 AC2 ALA B 55 TYR B 66 1 12
HELIX 21 AC3 VAL B 74 ILE B 79 1 6
HELIX 22 AC4 ASP B 84 GLY B 103 1 20
HELIX 23 AC5 SER B 115 VAL B 117 5 3
HELIX 24 AC6 SER B 118 CYS B 129 1 12
HELIX 25 AC7 ARG B 132 HIS B 138 1 7
HELIX 26 AC8 LEU B 139 THR B 146 1 8
HELIX 27 AC9 THR B 154 LEU B 170 1 17
HELIX 28 AD1 GLY B 179 ASP B 181 5 3
HELIX 29 AD2 GLN B 182 GLY B 201 1 20
HELIX 30 AD3 ASP B 233 THR B 237 5 5
HELIX 31 AD4 SER B 243 ALA B 254 1 12
HELIX 32 AD5 ARG B 269 GLY B 284 1 16
HELIX 33 AD6 SER B 286 SER B 294 1 9
HELIX 34 AD7 ASN B 298 LYS B 325 1 28
HELIX 35 AD8 ASP B 327 GLY B 358 1 32
SHEET 1 AA1 3 VAL A 37 ILE A 41 0
SHEET 2 AA1 3 VAL A 69 ILE A 73 1 O LEU A 70 N VAL A 37
SHEET 3 AA1 3 ILE A 110 GLN A 113 1 O ILE A 110 N TYR A 71
SHEET 1 AA2 2 HIS A 175 PRO A 177 0
SHEET 2 AA2 2 GLU A 208 ILE A 210 1 O GLU A 208 N VAL A 176
SHEET 1 AA3 3 VAL B 37 ILE B 41 0
SHEET 2 AA3 3 VAL B 69 ILE B 73 1 O LEU B 70 N VAL B 37
SHEET 3 AA3 3 ILE B 110 GLN B 113 1 O ILE B 110 N TYR B 71
SHEET 1 AA4 2 HIS B 175 PRO B 177 0
SHEET 2 AA4 2 GLU B 208 ILE B 210 1 O GLU B 208 N VAL B 176
LINK OE1 GLU A 312 MN MN A 404 1555 1555 2.24
LINK OE1 GLU A 312 MN MN A 404 1555 2555 2.28
LINK O3G ATP A 402 MN MN A 403 1555 1555 2.08
LINK O2B ATP A 402 MN MN A 403 1555 1555 2.11
LINK O2A ATP A 402 MN MN A 403 1555 1555 2.18
LINK MN MN A 403 O HOH A 529 1555 1555 2.17
LINK MN MN A 403 O HOH A 555 1555 1555 2.19
LINK MN MN A 403 O HOH A 691 1555 1555 2.18
LINK MN MN A 404 O HOH A 533 1555 1555 2.20
LINK MN MN A 404 O HOH A 533 1555 2555 2.18
LINK MN MN A 404 O HOH A 703 1555 1555 2.18
LINK MN MN A 404 O HOH A 703 1555 2555 2.22
LINK OE1 GLU B 312 MN MN B 404 1555 1555 2.12
LINK OE1 GLU B 312 MN MN B 404 1555 2756 2.28
LINK O1G ATP B 402 MN MN B 403 1555 1555 2.04
LINK O1B ATP B 402 MN MN B 403 1555 1555 2.14
LINK O2A ATP B 402 MN MN B 403 1555 1555 2.17
LINK MN MN B 403 O HOH B 522 1555 1555 2.18
LINK MN MN B 403 O HOH B 618 1555 1555 2.20
LINK MN MN B 403 O HOH B 678 1555 1555 2.18
LINK MN MN B 404 O HOH B 511 1555 1555 2.01
LINK MN MN B 404 O HOH B 511 1555 2756 2.16
LINK MN MN B 404 O HOH B 705 1555 1555 2.20
LINK MN MN B 404 O HOH B 705 1555 2756 2.42
SITE 1 AC1 12 PHE A 38 SER A 39 GLY A 40 GLN A 42
SITE 2 AC1 12 HIS A 77 TYR A 160 GLN A 164 ASP A 167
SITE 3 AC1 12 GLN A 182 ATP A 402 HOH A 529 HOH A 555
SITE 1 AC2 28 ILE A 41 GLN A 42 HIS A 48 GLY A 50
SITE 2 AC2 28 ASN A 51 GLY A 54 VAL A 178 GLY A 179
SITE 3 AC2 28 ASP A 181 GLN A 182 MET A 214 LYS A 215
SITE 4 AC2 28 LYS A 216 VAL A 217 LYS A 226 MET A 227
SITE 5 AC2 28 SER A 228 LYS A 229 SER A 230 5BX A 401
SITE 6 AC2 28 MN A 403 HOH A 517 HOH A 529 HOH A 530
SITE 7 AC2 28 HOH A 555 HOH A 605 HOH A 689 HOH A 691
SITE 1 AC3 4 ATP A 402 HOH A 529 HOH A 555 HOH A 691
SITE 1 AC4 3 GLU A 312 HOH A 533 HOH A 703
SITE 1 AC5 15 PHE B 38 GLY B 40 GLN B 42 VAL B 74
SITE 2 AC5 15 HIS B 77 TYR B 160 GLN B 164 ASP B 167
SITE 3 AC5 15 ILE B 168 VAL B 176 VAL B 178 GLN B 182
SITE 4 AC5 15 ATP B 402 HOH B 522 HOH B 618
SITE 1 AC6 29 ILE B 41 GLN B 42 HIS B 48 GLY B 50
SITE 2 AC6 29 ASN B 51 GLY B 54 VAL B 178 GLY B 179
SITE 3 AC6 29 ASP B 181 GLN B 182 MET B 214 LYS B 215
SITE 4 AC6 29 LYS B 216 VAL B 217 LYS B 226 MET B 227
SITE 5 AC6 29 SER B 228 LYS B 229 SER B 230 5BX B 401
SITE 6 AC6 29 MN B 403 HOH B 522 HOH B 525 HOH B 571
SITE 7 AC6 29 HOH B 595 HOH B 611 HOH B 618 HOH B 630
SITE 8 AC6 29 HOH B 678
SITE 1 AC7 4 ATP B 402 HOH B 522 HOH B 618 HOH B 678
SITE 1 AC8 3 GLU B 312 HOH B 511 HOH B 705
SITE 1 AC9 7 THR A 121 SER A 124 TRP A 125 THR B 121
SITE 2 AC9 7 SER B 124 TRP B 125 HOH B 582
SITE 1 AD1 4 GLU B 344 TYR B 347 HOH B 637 HOH B 670
CRYST1 58.289 78.087 153.996 90.00 96.55 90.00 C 1 2 1 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.017156 0.000000 0.001970 0.00000
SCALE2 0.000000 0.012806 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006536 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
