HEADER HYDROLASE 23-MAY-07 2Q16
TITLE STRUCTURE OF THE E. COLI INOSINE TRIPHOSPHATE PYROPHOSPHATASE RGDB IN
TITLE 2 COMPLEX WITH ITP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HAM1 PROTEIN HOMOLOG;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 3.6.1.19;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 83333;
SOURCE 4 STRAIN: K12;
SOURCE 5 GENE: YGGV;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RP;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15-B-BASED P11
KEYWDS ITP PYROPHOSPHATASE X-RAY STRUCTURE ENZYME MECHANISM SUBSTRATE,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.U.SINGER,R.LAM,M.PROUDFOOT,T.SKARINA,A.SAVCHENKO,A.F.YAKUNIN
REVDAT 5 21-FEB-24 2Q16 1 REMARK
REVDAT 4 20-OCT-21 2Q16 1 REMARK SEQADV
REVDAT 3 13-JUL-11 2Q16 1 VERSN
REVDAT 2 24-FEB-09 2Q16 1 VERSN
REVDAT 1 19-FEB-08 2Q16 0
JRNL AUTH A.SAVCHENKO,M.PROUDFOOT,T.SKARINA,A.SINGER,O.LITVINOVA,
JRNL AUTH 2 R.SANISHVILI,G.BROWN,N.CHIRGADZE,A.F.YAKUNIN
JRNL TITL MOLECULAR BASIS OF THE ANTIMUTAGENIC ACTIVITY OF THE
JRNL TITL 2 HOUSE-CLEANING INOSINE TRIPHOSPHATE PYROPHOSPHATASE RDGB
JRNL TITL 3 FROM ESCHERICHIA COLI.
JRNL REF J.MOL.BIOL. V. 374 1091 2007
JRNL REFN ISSN 0022-2836
JRNL PMID 17976651
JRNL DOI 10.1016/J.JMB.2007.10.012
REMARK 2
REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.98
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 34514
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.173
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1813
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2510
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96
REMARK 3 BIN R VALUE (WORKING SET) : 0.1760
REMARK 3 BIN FREE R VALUE SET COUNT : 121
REMARK 3 BIN FREE R VALUE : 0.2180
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2922
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 74
REMARK 3 SOLVENT ATOMS : 410
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 24.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.73
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.01000
REMARK 3 B22 (A**2) : -0.01000
REMARK 3 B33 (A**2) : 0.01000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.137
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.965
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3058 ; 0.014 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4168 ; 1.678 ; 2.002
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ;10.601 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;32.998 ;24.160
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 491 ;13.263 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.060 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 477 ; 0.123 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2290 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1487 ; 0.217 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2089 ; 0.304 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 310 ; 0.208 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.191 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.152 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.218 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1938 ; 0.833 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3095 ; 1.502 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1145 ; 2.518 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1072 ; 4.087 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 197
REMARK 3 ORIGIN FOR THE GROUP (A): 33.7758 7.5914 11.8241
REMARK 3 T TENSOR
REMARK 3 T11: -0.1505 T22: -0.0908
REMARK 3 T33: -0.1058 T12: 0.0046
REMARK 3 T13: 0.0110 T23: 0.0249
REMARK 3 L TENSOR
REMARK 3 L11: 1.0008 L22: 2.0608
REMARK 3 L33: 1.8079 L12: -0.0762
REMARK 3 L13: 0.5768 L23: 0.3253
REMARK 3 S TENSOR
REMARK 3 S11: 0.0415 S12: -0.0043 S13: 0.0196
REMARK 3 S21: -0.0823 S22: -0.0664 S23: -0.0923
REMARK 3 S31: 0.0573 S32: -0.0873 S33: 0.0248
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 3 B 195
REMARK 3 ORIGIN FOR THE GROUP (A): 33.8441 8.5572 42.9215
REMARK 3 T TENSOR
REMARK 3 T11: -0.0748 T22: -0.1141
REMARK 3 T33: -0.1191 T12: 0.0442
REMARK 3 T13: 0.0017 T23: 0.0200
REMARK 3 L TENSOR
REMARK 3 L11: 1.7000 L22: 1.6476
REMARK 3 L33: 2.0238 L12: -0.2710
REMARK 3 L13: -1.3069 L23: 0.6599
REMARK 3 S TENSOR
REMARK 3 S11: -0.0385 S12: 0.0003 S13: -0.1336
REMARK 3 S21: 0.0461 S22: -0.0229 S23: 0.0292
REMARK 3 S31: 0.0786 S32: -0.0589 S33: 0.0613
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2Q16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-07.
REMARK 100 THE DEPOSITION ID IS D_1000043019.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-DEC-06
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942
REMARK 200 MONOCHROMATOR : YALE MIRRORS
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36385
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950
REMARK 200 RESOLUTION RANGE LOW (A) : 500.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 19.40
REMARK 200 R MERGE (I) : 0.08900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 17.70
REMARK 200 R MERGE FOR SHELL (I) : 0.55100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.29
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4K, 200 MM AMMONIUM SULFATE,
REMARK 280 100 MM SODIUM ACETATE, 2% ISO-PROPANOL, 20 MM CALCIUM CHLORIDE,
REMARK 280 10MM ITP, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2
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 -Y+1/2,X+1/2,Z
REMARK 290 4555 Y+1/2,-X+1/2,Z
REMARK 290 5555 -X+1/2,Y+1/2,-Z
REMARK 290 6555 X+1/2,-Y+1/2,-Z
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 60.32300
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.32300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.32300
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.32300
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.32300
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.32300
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.32300
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.32300
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 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 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 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 MSE A -19
REMARK 465 GLY A -18
REMARK 465 SER A -17
REMARK 465 SER A -16
REMARK 465 HIS A -15
REMARK 465 HIS A -14
REMARK 465 HIS A -13
REMARK 465 HIS A -12
REMARK 465 HIS A -11
REMARK 465 HIS A -10
REMARK 465 SER A -9
REMARK 465 SER A -8
REMARK 465 GLY A -7
REMARK 465 LEU A -6
REMARK 465 VAL A -5
REMARK 465 PRO A -4
REMARK 465 ARG A -3
REMARK 465 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 GLY A 198
REMARK 465 SER A 199
REMARK 465 MSE B -19
REMARK 465 GLY B -18
REMARK 465 SER B -17
REMARK 465 SER B -16
REMARK 465 HIS B -15
REMARK 465 HIS B -14
REMARK 465 HIS B -13
REMARK 465 HIS B -12
REMARK 465 HIS B -11
REMARK 465 HIS B -10
REMARK 465 SER B -9
REMARK 465 SER B -8
REMARK 465 GLY B -7
REMARK 465 LEU B -6
REMARK 465 VAL B -5
REMARK 465 PRO B -4
REMARK 465 ARG B -3
REMARK 465 GLY B -2
REMARK 465 SER B -1
REMARK 465 HIS B 0
REMARK 465 MSE B 1
REMARK 465 GLN B 2
REMARK 465 ASN B 196
REMARK 465 GLY B 197
REMARK 465 GLY B 198
REMARK 465 SER B 199
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 MSE A 1 CG SE CE
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 O HOH A 6306 O HOH A 6398 2.05
REMARK 500 NH1 ARG B 146 O HOH B 216 2.08
REMARK 500 NH2 ARG A 87 O HOH A 6393 2.09
REMARK 500 O HOH A 6277 O HOH A 6279 2.12
REMARK 500 O HOH B 283 O HOH B 306 2.14
REMARK 500 O HOH A 6294 O HOH A 6299 2.15
REMARK 500 O HOH B 325 O HOH B 335 2.18
REMARK 500 OG SER A 178 O HOH A 6334 2.18
REMARK 500 O HOH B 286 O HOH B 292 2.19
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 LEU A 103 -75.16 -5.69
REMARK 500 LEU B 103 -73.77 1.86
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 LEU A 102 LEU A 103 128.77
REMARK 500 LEU B 102 LEU B 103 121.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6245
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ITT A 6246
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ITT B 203
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1K7K RELATED DB: PDB
REMARK 900 STRUCTURE OF APO-RGDB
REMARK 900 RELATED ID: 2PYU RELATED DB: PDB
REMARK 900 RGDB IN COMPLEX WITH IMP
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THESE RESIDUES BELONG TO A TEV CLEAVAGE SITE.
DBREF 2Q16 A 1 197 UNP P52061 HAM1_ECOLI 1 197
DBREF 2Q16 B 1 197 UNP P52061 HAM1_ECOLI 1 197
SEQADV 2Q16 MSE A -19 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 GLY A -18 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER A -17 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER A -16 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS A -15 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS A -14 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS A -13 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS A -12 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS A -11 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS A -10 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER A -9 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER A -8 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 GLY A -7 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 LEU A -6 UNP P52061 SEE REMARK 999
SEQADV 2Q16 VAL A -5 UNP P52061 SEE REMARK 999
SEQADV 2Q16 PRO A -4 UNP P52061 SEE REMARK 999
SEQADV 2Q16 ARG A -3 UNP P52061 SEE REMARK 999
SEQADV 2Q16 GLY A -2 UNP P52061 SEE REMARK 999
SEQADV 2Q16 SER A -1 UNP P52061 SEE REMARK 999
SEQADV 2Q16 HIS A 0 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 MSE A 1 UNP P52061 MET 1 MODIFIED RESIDUE
SEQADV 2Q16 ALA A 69 UNP P52061 ASP 69 ENGINEERED MUTATION
SEQADV 2Q16 MSE A 106 UNP P52061 MET 106 MODIFIED RESIDUE
SEQADV 2Q16 GLY A 198 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER A 199 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 MSE B -19 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 GLY B -18 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER B -17 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER B -16 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS B -15 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS B -14 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS B -13 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS B -12 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS B -11 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 HIS B -10 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER B -9 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER B -8 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 GLY B -7 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 LEU B -6 UNP P52061 SEE REMARK 999
SEQADV 2Q16 VAL B -5 UNP P52061 SEE REMARK 999
SEQADV 2Q16 PRO B -4 UNP P52061 SEE REMARK 999
SEQADV 2Q16 ARG B -3 UNP P52061 SEE REMARK 999
SEQADV 2Q16 GLY B -2 UNP P52061 SEE REMARK 999
SEQADV 2Q16 SER B -1 UNP P52061 SEE REMARK 999
SEQADV 2Q16 HIS B 0 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 MSE B 1 UNP P52061 MET 1 MODIFIED RESIDUE
SEQADV 2Q16 ALA B 69 UNP P52061 ASP 69 ENGINEERED MUTATION
SEQADV 2Q16 MSE B 106 UNP P52061 MET 106 MODIFIED RESIDUE
SEQADV 2Q16 GLY B 198 UNP P52061 EXPRESSION TAG
SEQADV 2Q16 SER B 199 UNP P52061 EXPRESSION TAG
SEQRES 1 A 219 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 219 LEU VAL PRO ARG GLY SER HIS MSE GLN LYS VAL VAL LEU
SEQRES 3 A 219 ALA THR GLY ASN VAL GLY LYS VAL ARG GLU LEU ALA SER
SEQRES 4 A 219 LEU LEU SER ASP PHE GLY LEU ASP ILE VAL ALA GLN THR
SEQRES 5 A 219 ASP LEU GLY VAL ASP SER ALA GLU GLU THR GLY LEU THR
SEQRES 6 A 219 PHE ILE GLU ASN ALA ILE LEU LYS ALA ARG HIS ALA ALA
SEQRES 7 A 219 LYS VAL THR ALA LEU PRO ALA ILE ALA ASP ALA SER GLY
SEQRES 8 A 219 LEU ALA VAL ASP VAL LEU GLY GLY ALA PRO GLY ILE TYR
SEQRES 9 A 219 SER ALA ARG TYR SER GLY GLU ASP ALA THR ASP GLN LYS
SEQRES 10 A 219 ASN LEU GLN LYS LEU LEU GLU THR MSE LYS ASP VAL PRO
SEQRES 11 A 219 ASP ASP GLN ARG GLN ALA ARG PHE HIS CYS VAL LEU VAL
SEQRES 12 A 219 TYR LEU ARG HIS ALA GLU ASP PRO THR PRO LEU VAL CYS
SEQRES 13 A 219 HIS GLY SER TRP PRO GLY VAL ILE THR ARG GLU PRO ALA
SEQRES 14 A 219 GLY THR GLY GLY PHE GLY TYR ASP PRO ILE PHE PHE VAL
SEQRES 15 A 219 PRO SER GLU GLY LYS THR ALA ALA GLU LEU THR ARG GLU
SEQRES 16 A 219 GLU LYS SER ALA ILE SER HIS ARG GLY GLN ALA LEU LYS
SEQRES 17 A 219 LEU LEU LEU ASP ALA LEU ARG ASN GLY GLY SER
SEQRES 1 B 219 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 B 219 LEU VAL PRO ARG GLY SER HIS MSE GLN LYS VAL VAL LEU
SEQRES 3 B 219 ALA THR GLY ASN VAL GLY LYS VAL ARG GLU LEU ALA SER
SEQRES 4 B 219 LEU LEU SER ASP PHE GLY LEU ASP ILE VAL ALA GLN THR
SEQRES 5 B 219 ASP LEU GLY VAL ASP SER ALA GLU GLU THR GLY LEU THR
SEQRES 6 B 219 PHE ILE GLU ASN ALA ILE LEU LYS ALA ARG HIS ALA ALA
SEQRES 7 B 219 LYS VAL THR ALA LEU PRO ALA ILE ALA ASP ALA SER GLY
SEQRES 8 B 219 LEU ALA VAL ASP VAL LEU GLY GLY ALA PRO GLY ILE TYR
SEQRES 9 B 219 SER ALA ARG TYR SER GLY GLU ASP ALA THR ASP GLN LYS
SEQRES 10 B 219 ASN LEU GLN LYS LEU LEU GLU THR MSE LYS ASP VAL PRO
SEQRES 11 B 219 ASP ASP GLN ARG GLN ALA ARG PHE HIS CYS VAL LEU VAL
SEQRES 12 B 219 TYR LEU ARG HIS ALA GLU ASP PRO THR PRO LEU VAL CYS
SEQRES 13 B 219 HIS GLY SER TRP PRO GLY VAL ILE THR ARG GLU PRO ALA
SEQRES 14 B 219 GLY THR GLY GLY PHE GLY TYR ASP PRO ILE PHE PHE VAL
SEQRES 15 B 219 PRO SER GLU GLY LYS THR ALA ALA GLU LEU THR ARG GLU
SEQRES 16 B 219 GLU LYS SER ALA ILE SER HIS ARG GLY GLN ALA LEU LYS
SEQRES 17 B 219 LEU LEU LEU ASP ALA LEU ARG ASN GLY GLY SER
MODRES 2Q16 MSE A 1 MET SELENOMETHIONINE
MODRES 2Q16 MSE A 106 MET SELENOMETHIONINE
MODRES 2Q16 MSE B 106 MET SELENOMETHIONINE
HET MSE A 1 5
HET MSE A 106 8
HET MSE B 106 8
HET CA A 200 1
HET NA A 201 1
HET NA A 202 1
HET NA A 203 1
HET SO4 A6245 5
HET ITT A6246 31
HET CA B 200 1
HET NA B 201 1
HET NA B 202 1
HET ITT B 203 31
HETNAM MSE SELENOMETHIONINE
HETNAM CA CALCIUM ION
HETNAM NA SODIUM ION
HETNAM SO4 SULFATE ION
HETNAM ITT INOSINE 5'-TRIPHOSPHATE
HETSYN ITT INOSINE TRIPHOSPHATE
FORMUL 1 MSE 3(C5 H11 N O2 SE)
FORMUL 3 CA 2(CA 2+)
FORMUL 4 NA 5(NA 1+)
FORMUL 7 SO4 O4 S 2-
FORMUL 8 ITT 2(C10 H15 N4 O14 P3)
FORMUL 13 HOH *410(H2 O)
HELIX 1 1 ASN A 10 GLY A 25 1 16
HELIX 2 2 THR A 32 GLY A 35 5 4
HELIX 3 3 THR A 45 ALA A 62 1 18
HELIX 4 4 VAL A 76 GLY A 78 5 3
HELIX 5 5 PRO A 81 SER A 85 5 5
HELIX 6 6 THR A 94 MSE A 106 1 13
HELIX 7 7 PRO A 110 GLN A 113 5 4
HELIX 8 8 TYR A 156 PRO A 158 5 3
HELIX 9 9 THR A 168 LEU A 172 5 5
HELIX 10 10 THR A 173 SER A 181 1 9
HELIX 11 11 SER A 181 ASN A 196 1 16
HELIX 12 12 ASN B 10 GLY B 25 1 16
HELIX 13 13 THR B 32 GLY B 35 5 4
HELIX 14 14 THR B 45 ALA B 62 1 18
HELIX 15 15 VAL B 76 GLY B 78 5 3
HELIX 16 16 PRO B 81 SER B 85 5 5
HELIX 17 17 THR B 94 MSE B 106 1 13
HELIX 18 18 PRO B 110 GLN B 113 5 4
HELIX 19 19 TYR B 156 PRO B 158 5 3
HELIX 20 20 THR B 168 LEU B 172 5 5
HELIX 21 21 THR B 173 SER B 181 1 9
HELIX 22 22 SER B 181 ARG B 195 1 15
SHEET 1 A 6 ASP A 27 ALA A 30 0
SHEET 2 A 6 LYS A 3 LEU A 6 1 N VAL A 4 O ASP A 27
SHEET 3 A 6 ALA A 65 VAL A 74 1 O ILE A 66 N VAL A 5
SHEET 4 A 6 GLN A 115 LEU A 125 -1 O ARG A 117 N ALA A 73
SHEET 5 A 6 LEU A 134 ILE A 144 -1 O CYS A 136 N LEU A 122
SHEET 6 A 6 PHE A 160 PHE A 161 -1 O PHE A 161 N VAL A 143
SHEET 1 B 6 ILE B 28 ALA B 30 0
SHEET 2 B 6 VAL B 4 LEU B 6 1 N LEU B 6 O VAL B 29
SHEET 3 B 6 ALA B 65 VAL B 74 1 O ILE B 66 N VAL B 5
SHEET 4 B 6 GLN B 115 LEU B 125 -1 O ARG B 117 N ALA B 73
SHEET 5 B 6 LEU B 134 ILE B 144 -1 O CYS B 136 N LEU B 122
SHEET 6 B 6 PHE B 160 PHE B 161 -1 O PHE B 161 N VAL B 143
CISPEP 1 ALA A 80 PRO A 81 0 -5.57
CISPEP 2 ALA B 80 PRO B 81 0 -2.25
SITE 1 AC1 4 GLU A 41 ITT A6246 HOH A6450 HOH A6455
SITE 1 AC2 5 ASN A 10 ASP A 95 PHE A 154 ITT A6246
SITE 2 AC2 5 HOH A6268
SITE 1 AC3 5 ILE A 83 SER A 85 ALA A 86 ITT A6246
SITE 2 AC3 5 HOH A6372
SITE 1 AC4 2 GLU A 16 SER A 181
SITE 1 AC5 3 ARG A 195 ASP B 75 ARG B 117
SITE 1 AC6 3 GLU B 41 ITT B 203 HOH B 347
SITE 1 AC7 4 ASN B 10 ASP B 95 ITT B 203 HOH B 237
SITE 1 AC8 5 ASP B 95 ASN B 98 TYR B 156 ITT B 203
SITE 2 AC8 5 HOH B 227
SITE 1 AC9 30 THR A 8 GLY A 9 ASN A 10 LYS A 13
SITE 2 AC9 30 GLU A 41 LYS A 53 ASP A 68 ALA A 69
SITE 3 AC9 30 SER A 70 GLY A 71 SER A 85 ALA A 86
SITE 4 AC9 30 PHE A 118 PHE A 154 GLY A 155 TYR A 156
SITE 5 AC9 30 ASP A 157 LYS A 177 HIS A 182 ARG A 183
SITE 6 AC9 30 CA A 200 NA A 201 NA A 202 HOH A6251
SITE 7 AC9 30 HOH A6268 HOH A6274 HOH A6323 HOH A6328
SITE 8 AC9 30 HOH A6450 HOH A6455
SITE 1 BC1 28 THR B 8 GLY B 9 ASN B 10 LYS B 13
SITE 2 BC1 28 GLU B 41 LYS B 53 ASP B 68 ALA B 69
SITE 3 BC1 28 SER B 70 GLY B 71 SER B 85 ALA B 86
SITE 4 BC1 28 PHE B 118 PHE B 154 GLY B 155 TYR B 156
SITE 5 BC1 28 ASP B 157 LYS B 177 HIS B 182 ARG B 183
SITE 6 BC1 28 CA B 200 NA B 201 NA B 202 HOH B 232
SITE 7 BC1 28 HOH B 237 HOH B 264 HOH B 360 HOH B 364
CRYST1 120.646 120.646 66.562 90.00 90.00 90.00 P 4 21 2 16
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 0.008289 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008289 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015024 0.00000
HETATM 1 N MSE A 1 39.832 34.044 15.275 1.00 47.84 N
HETATM 2 CA MSE A 1 40.984 34.082 16.228 1.00 47.03 C
HETATM 3 C MSE A 1 41.415 32.666 16.610 1.00 46.61 C
HETATM 4 O MSE A 1 42.257 32.082 15.921 1.00 46.87 O
HETATM 5 CB MSE A 1 40.643 34.911 17.468 1.00 47.56 C
(ATOM LINES ARE NOT SHOWN.)
END
