HEADER OXIDOREDUCTASE 12-FEB-15 4Y67
TITLE STRUCTURE OF PLASMODIUM FALCIPARUM DXR IN COMPLEX WITH A BETA-
TITLE 2 SUBSTITUTED FOSMIDOMYCIN ANALOGUE, RC176, AND MANGANESE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE,
COMPND 3 APICOPLAST;
COMPND 4 CHAIN: A, B;
COMPND 5 SYNONYM: DXP REDUCTOISOMERASE;
COMPND 6 EC: 1.1.1.267;
COMPND 7 ENGINEERED: YES;
COMPND 8 OTHER_DETAILS: MATURE PROTEIN LACKS SIGNAL AND APICOPLAST TARGETING
COMPND 9 SEQUENCES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM;
SOURCE 3 ORGANISM_TAXID: 36329;
SOURCE 4 STRAIN: 3D7;
SOURCE 5 GENE: DXR, PF14_0641;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C43;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEXP-5-CT/TOPO
KEYWDS ENZYME-INHIBITOR COMPLEX, MEP PATHWAY, ISOPRENOID BIOSYNTHESIS,
KEYWDS 2 OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SOORIYAARACHCHI,T.BERGFORS,T.A.JONES,S.L.MOWBRAY
REVDAT 3 10-JAN-24 4Y67 1 LINK
REVDAT 2 22-APR-15 4Y67 1 JRNL
REVDAT 1 01-APR-15 4Y67 0
JRNL AUTH R.CHOFOR,S.SOORIYAARACHCHI,M.D.RISSEEUW,T.BERGFORS,J.POUYEZ,
JRNL AUTH 2 C.JOHNY,A.HAYMOND,A.EVERAERT,C.S.DOWD,L.MAES,T.COENYE,
JRNL AUTH 3 A.ALEX,R.D.COUCH,T.A.JONES,J.WOUTERS,S.L.MOWBRAY,
JRNL AUTH 4 S.VAN CALENBERGH
JRNL TITL SYNTHESIS AND BIOACTIVITY OF BETA-SUBSTITUTED FOSMIDOMYCIN
JRNL TITL 2 ANALOGUES TARGETING 1-DEOXY-D-XYLULOSE-5-PHOSPHATE
JRNL TITL 3 REDUCTOISOMERASE.
JRNL REF J.MED.CHEM. V. 58 2988 2015
JRNL REFN ISSN 0022-2623
JRNL PMID 25781377
JRNL DOI 10.1021/JM5014264
REMARK 2
REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
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) : 1.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.65
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2
REMARK 3 NUMBER OF REFLECTIONS : 104856
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) : 0.178
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 5530
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) : 1.60
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64
REMARK 3 REFLECTION IN BIN (WORKING SET) : 7345
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40
REMARK 3 BIN R VALUE (WORKING SET) : 0.2650
REMARK 3 BIN FREE R VALUE SET COUNT : 388
REMARK 3 BIN FREE R VALUE : 0.2820
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6552
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 44
REMARK 3 SOLVENT ATOMS : 714
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.63
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.03000
REMARK 3 B22 (A**2) : 0.07000
REMARK 3 B33 (A**2) : 1.68000
REMARK 3 B12 (A**2) : -0.71000
REMARK 3 B13 (A**2) : 0.23000
REMARK 3 B23 (A**2) : -1.59000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.092
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.284
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6831 ; 0.011 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 6629 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9237 ; 1.329 ; 1.956
REMARK 3 BOND ANGLES OTHERS (DEGREES): 15347 ; 0.766 ; 2.994
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 848 ; 5.525 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 302 ;37.499 ;26.424
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1289 ;16.587 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;14.580 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1053 ; 0.079 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7680 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1494 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): 3335 ; 1.482 ; 2.020
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3334 ; 1.481 ; 2.019
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4184 ; 2.321 ; 3.020
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4185 ; 2.321 ; 3.022
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3496 ; 2.128 ; 2.351
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3497 ; 2.127 ; 2.351
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5048 ; 3.470 ; 3.408
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8595 ; 5.773 ;17.787
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8284 ; 5.586 ;17.354
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 : 1
REMARK 3
REMARK 3 NCS GROUP NUMBER : 1
REMARK 3 CHAIN NAMES : A B
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 77 A 486 1
REMARK 3 1 B 77 B 486 1
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 TIGHT THERMAL 1 A (A**2): 3948 ; 2.29 ; 0.50
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 4Y67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-FEB-15.
REMARK 100 THE DEPOSITION ID IS D_1000206403.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856
REMARK 200 MONOCHROMATOR : SI(311)
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 110454
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
REMARK 200 RESOLUTION RANGE LOW (A) : 79.970
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.47800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 3AU8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 8000, 20% V/V ETHYLENE
REMARK 280 GLYCOL, 0.02M EACH OF SODIUM L-GLUTAMATE, DL-ALANINE, GLYCINE,
REMARK 280 DL-LYSINE HCL, DL-SERINE, 0.1M MES/IMIDAZOLE PH 6.5, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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: 3790 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 32600 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 MET A 67
REMARK 465 ALA A 68
REMARK 465 HIS A 69
REMARK 465 HIS A 70
REMARK 465 HIS A 71
REMARK 465 HIS A 72
REMARK 465 HIS A 73
REMARK 465 HIS A 74
REMARK 465 LYS A 75
REMARK 465 LYS A 76
REMARK 465 SER A 487
REMARK 465 SER A 488
REMARK 465 MET B 67
REMARK 465 ALA B 68
REMARK 465 HIS B 69
REMARK 465 HIS B 70
REMARK 465 HIS B 71
REMARK 465 HIS B 72
REMARK 465 HIS B 73
REMARK 465 HIS B 74
REMARK 465 LYS B 75
REMARK 465 LYS B 76
REMARK 465 SER B 487
REMARK 465 SER B 488
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 NE2 GLN A 253 O HOH A 844 1.34
REMARK 500 O HOH B 601 O HOH B 640 1.56
REMARK 500 O HOH A 714 O HOH A 875 1.64
REMARK 500 OD1 ASN B 284 O HOH B 601 1.65
REMARK 500 O HOH B 705 O HOH B 859 1.80
REMARK 500 N PRO A 77 O HOH A 891 1.83
REMARK 500 O HOH A 833 O HOH A 933 1.85
REMARK 500 O HOH B 793 O HOH B 914 1.86
REMARK 500 O HOH B 781 O HOH B 824 1.96
REMARK 500 OD1 ASN A 92 O HOH A 951 1.98
REMARK 500 O HOH B 826 O HOH B 838 1.98
REMARK 500 O HOH A 875 O HOH A 927 2.02
REMARK 500 O HOH B 773 O HOH B 807 2.05
REMARK 500 O ILE A 179 O HOH A 956 2.06
REMARK 500 NZ LYS B 484 O HOH B 602 2.07
REMARK 500 O HOH A 755 O HOH A 946 2.07
REMARK 500 O HOH B 672 O HOH B 680 2.09
REMARK 500 OE1 GLU B 449 O HOH B 922 2.11
REMARK 500 NE2 GLN A 469 O HOH A 906 2.11
REMARK 500 O HOH A 922 O HOH A 936 2.14
REMARK 500 O HOH A 760 O HOH A 946 2.14
REMARK 500 O HOH B 838 O HOH B 867 2.15
REMARK 500 O HOH A 827 O HOH A 927 2.16
REMARK 500 OE1 GLU B 142 O HOH B 603 2.16
REMARK 500 O HOH B 720 O HOH B 921 2.17
REMARK 500 O HOH A 773 O HOH A 945 2.17
REMARK 500 OG SER A 457 O HOH A 876 2.18
REMARK 500 O HOH A 844 O HOH A 938 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 O HOH A 602 O HOH B 666 1666 2.11
REMARK 500 O HOH A 611 O HOH A 681 1655 2.18
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 ASN A 115 -71.66 -70.60
REMARK 500 SER A 183 -132.13 55.33
REMARK 500 THR A 249 -152.77 -144.57
REMARK 500 SER A 342 169.43 166.47
REMARK 500 LYS A 349 2.75 85.02
REMARK 500 ASP A 359 115.00 -174.38
REMARK 500 SER A 387 -50.01 77.14
REMARK 500 ASN A 413 -141.97 49.03
REMARK 500 SER B 183 -139.28 54.49
REMARK 500 THR B 249 -154.90 -148.11
REMARK 500 ASN B 255 9.04 81.22
REMARK 500 SER B 342 168.44 169.53
REMARK 500 LYS B 349 3.41 82.72
REMARK 500 ASP B 359 112.41 -170.40
REMARK 500 SER B 387 -47.95 80.15
REMARK 500 ASN B 413 -138.20 47.61
REMARK 500
REMARK 500 REMARK: NULL
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 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 231 OD1
REMARK 620 2 GLU A 233 OE1 97.5
REMARK 620 3 GLU A 315 OE2 100.6 96.6
REMARK 620 4 RC5 A 501 O12 127.4 134.4 84.2
REMARK 620 5 RC5 A 501 O10 84.0 103.2 159.0 77.0
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN B 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 231 OD1
REMARK 620 2 GLU B 233 OE1 97.4
REMARK 620 3 GLU B 315 OE2 99.1 97.4
REMARK 620 4 RC5 B 501 O12 124.3 137.3 85.6
REMARK 620 5 RC5 B 501 O10 82.2 101.3 160.9 78.2
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue RC5 A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue RC5 B 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 502
DBREF 4Y67 A 75 488 UNP Q8IKG4 DXR_PLAF7 75 488
DBREF 4Y67 B 75 488 UNP Q8IKG4 DXR_PLAF7 75 488
SEQADV 4Y67 MET A 67 UNP Q8IKG4 INITIATING METHIONINE
SEQADV 4Y67 ALA A 68 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS A 69 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS A 70 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS A 71 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS A 72 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS A 73 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS A 74 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 MET B 67 UNP Q8IKG4 INITIATING METHIONINE
SEQADV 4Y67 ALA B 68 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS B 69 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS B 70 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS B 71 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS B 72 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS B 73 UNP Q8IKG4 EXPRESSION TAG
SEQADV 4Y67 HIS B 74 UNP Q8IKG4 EXPRESSION TAG
SEQRES 1 A 422 MET ALA HIS HIS HIS HIS HIS HIS LYS LYS PRO ILE ASN
SEQRES 2 A 422 VAL ALA ILE PHE GLY SER THR GLY SER ILE GLY THR ASN
SEQRES 3 A 422 ALA LEU ASN ILE ILE ARG GLU CYS ASN LYS ILE GLU ASN
SEQRES 4 A 422 VAL PHE ASN VAL LYS ALA LEU TYR VAL ASN LYS SER VAL
SEQRES 5 A 422 ASN GLU LEU TYR GLU GLN ALA ARG GLU PHE LEU PRO GLU
SEQRES 6 A 422 TYR LEU CYS ILE HIS ASP LYS SER VAL TYR GLU GLU LEU
SEQRES 7 A 422 LYS GLU LEU VAL LYS ASN ILE LYS ASP TYR LYS PRO ILE
SEQRES 8 A 422 ILE LEU CYS GLY ASP GLU GLY MET LYS GLU ILE CYS SER
SEQRES 9 A 422 SER ASN SER ILE ASP LYS ILE VAL ILE GLY ILE ASP SER
SEQRES 10 A 422 PHE GLN GLY LEU TYR SER THR MET TYR ALA ILE MET ASN
SEQRES 11 A 422 ASN LYS ILE VAL ALA LEU ALA ASN LYS GLU SER ILE VAL
SEQRES 12 A 422 SER ALA GLY PHE PHE LEU LYS LYS LEU LEU ASN ILE HIS
SEQRES 13 A 422 LYS ASN ALA LYS ILE ILE PRO VAL ASP SER GLU HIS SER
SEQRES 14 A 422 ALA ILE PHE GLN CYS LEU ASP ASN ASN LYS VAL LEU LYS
SEQRES 15 A 422 THR LYS CYS LEU GLN ASP ASN PHE SER LYS ILE ASN ASN
SEQRES 16 A 422 ILE ASN LYS ILE PHE LEU CYS SER SER GLY GLY PRO PHE
SEQRES 17 A 422 GLN ASN LEU THR MET ASP GLU LEU LYS ASN VAL THR SER
SEQRES 18 A 422 GLU ASN ALA LEU LYS HIS PRO LYS TRP LYS MET GLY LYS
SEQRES 19 A 422 LYS ILE THR ILE ASP SER ALA THR MET MET ASN LYS GLY
SEQRES 20 A 422 LEU GLU VAL ILE GLU THR HIS PHE LEU PHE ASP VAL ASP
SEQRES 21 A 422 TYR ASN ASP ILE GLU VAL ILE VAL HIS LYS GLU CYS ILE
SEQRES 22 A 422 ILE HIS SER CYS VAL GLU PHE ILE ASP LYS SER VAL ILE
SEQRES 23 A 422 SER GLN MET TYR TYR PRO ASP MET GLN ILE PRO ILE LEU
SEQRES 24 A 422 TYR SER LEU THR TRP PRO ASP ARG ILE LYS THR ASN LEU
SEQRES 25 A 422 LYS PRO LEU ASP LEU ALA GLN VAL SER THR LEU THR PHE
SEQRES 26 A 422 HIS LYS PRO SER LEU GLU HIS PHE PRO CYS ILE LYS LEU
SEQRES 27 A 422 ALA TYR GLN ALA GLY ILE LYS GLY ASN PHE TYR PRO THR
SEQRES 28 A 422 VAL LEU ASN ALA SER ASN GLU ILE ALA ASN ASN LEU PHE
SEQRES 29 A 422 LEU ASN ASN LYS ILE LYS TYR PHE ASP ILE SER SER ILE
SEQRES 30 A 422 ILE SER GLN VAL LEU GLU SER PHE ASN SER GLN LYS VAL
SEQRES 31 A 422 SER GLU ASN SER GLU ASP LEU MET LYS GLN ILE LEU GLN
SEQRES 32 A 422 ILE HIS SER TRP ALA LYS ASP LYS ALA THR ASP ILE TYR
SEQRES 33 A 422 ASN LYS HIS ASN SER SER
SEQRES 1 B 422 MET ALA HIS HIS HIS HIS HIS HIS LYS LYS PRO ILE ASN
SEQRES 2 B 422 VAL ALA ILE PHE GLY SER THR GLY SER ILE GLY THR ASN
SEQRES 3 B 422 ALA LEU ASN ILE ILE ARG GLU CYS ASN LYS ILE GLU ASN
SEQRES 4 B 422 VAL PHE ASN VAL LYS ALA LEU TYR VAL ASN LYS SER VAL
SEQRES 5 B 422 ASN GLU LEU TYR GLU GLN ALA ARG GLU PHE LEU PRO GLU
SEQRES 6 B 422 TYR LEU CYS ILE HIS ASP LYS SER VAL TYR GLU GLU LEU
SEQRES 7 B 422 LYS GLU LEU VAL LYS ASN ILE LYS ASP TYR LYS PRO ILE
SEQRES 8 B 422 ILE LEU CYS GLY ASP GLU GLY MET LYS GLU ILE CYS SER
SEQRES 9 B 422 SER ASN SER ILE ASP LYS ILE VAL ILE GLY ILE ASP SER
SEQRES 10 B 422 PHE GLN GLY LEU TYR SER THR MET TYR ALA ILE MET ASN
SEQRES 11 B 422 ASN LYS ILE VAL ALA LEU ALA ASN LYS GLU SER ILE VAL
SEQRES 12 B 422 SER ALA GLY PHE PHE LEU LYS LYS LEU LEU ASN ILE HIS
SEQRES 13 B 422 LYS ASN ALA LYS ILE ILE PRO VAL ASP SER GLU HIS SER
SEQRES 14 B 422 ALA ILE PHE GLN CYS LEU ASP ASN ASN LYS VAL LEU LYS
SEQRES 15 B 422 THR LYS CYS LEU GLN ASP ASN PHE SER LYS ILE ASN ASN
SEQRES 16 B 422 ILE ASN LYS ILE PHE LEU CYS SER SER GLY GLY PRO PHE
SEQRES 17 B 422 GLN ASN LEU THR MET ASP GLU LEU LYS ASN VAL THR SER
SEQRES 18 B 422 GLU ASN ALA LEU LYS HIS PRO LYS TRP LYS MET GLY LYS
SEQRES 19 B 422 LYS ILE THR ILE ASP SER ALA THR MET MET ASN LYS GLY
SEQRES 20 B 422 LEU GLU VAL ILE GLU THR HIS PHE LEU PHE ASP VAL ASP
SEQRES 21 B 422 TYR ASN ASP ILE GLU VAL ILE VAL HIS LYS GLU CYS ILE
SEQRES 22 B 422 ILE HIS SER CYS VAL GLU PHE ILE ASP LYS SER VAL ILE
SEQRES 23 B 422 SER GLN MET TYR TYR PRO ASP MET GLN ILE PRO ILE LEU
SEQRES 24 B 422 TYR SER LEU THR TRP PRO ASP ARG ILE LYS THR ASN LEU
SEQRES 25 B 422 LYS PRO LEU ASP LEU ALA GLN VAL SER THR LEU THR PHE
SEQRES 26 B 422 HIS LYS PRO SER LEU GLU HIS PHE PRO CYS ILE LYS LEU
SEQRES 27 B 422 ALA TYR GLN ALA GLY ILE LYS GLY ASN PHE TYR PRO THR
SEQRES 28 B 422 VAL LEU ASN ALA SER ASN GLU ILE ALA ASN ASN LEU PHE
SEQRES 29 B 422 LEU ASN ASN LYS ILE LYS TYR PHE ASP ILE SER SER ILE
SEQRES 30 B 422 ILE SER GLN VAL LEU GLU SER PHE ASN SER GLN LYS VAL
SEQRES 31 B 422 SER GLU ASN SER GLU ASP LEU MET LYS GLN ILE LEU GLN
SEQRES 32 B 422 ILE HIS SER TRP ALA LYS ASP LYS ALA THR ASP ILE TYR
SEQRES 33 B 422 ASN LYS HIS ASN SER SER
HET RC5 A 501 21
HET MN A 502 1
HET RC5 B 501 21
HET MN B 502 1
HETNAM RC5 [(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-
HETNAM 2 RC5 PHENYLPENTYL]PHOSPHONIC ACID
HETNAM MN MANGANESE (II) ION
FORMUL 3 RC5 2(C14 H22 N O5 P)
FORMUL 4 MN 2(MN 2+)
FORMUL 7 HOH *714(H2 O)
HELIX 1 AA1 GLY A 87 GLU A 104 1 18
HELIX 2 AA2 SER A 117 LEU A 129 1 13
HELIX 3 AA3 ASP A 137 SER A 139 5 3
HELIX 4 AA4 VAL A 140 LYS A 149 1 10
HELIX 5 AA5 GLY A 161 SER A 171 1 11
HELIX 6 AA6 ASP A 182 ASN A 196 1 15
HELIX 7 AA7 ASN A 204 HIS A 222 1 19
HELIX 8 AA8 ASP A 231 CYS A 240 1 10
HELIX 9 AA9 ASP A 242 LEU A 247 1 6
HELIX 10 AB1 ASN A 255 ASN A 260 1 6
HELIX 11 AB2 THR A 278 ASN A 284 1 7
HELIX 12 AB3 THR A 286 LYS A 292 1 7
HELIX 13 AB4 GLY A 299 MET A 309 1 11
HELIX 14 AB5 MET A 309 ASP A 324 1 16
HELIX 15 AB6 ASP A 326 ASN A 328 5 3
HELIX 16 AB7 MET A 360 TRP A 370 1 11
HELIX 17 AB8 ASP A 382 SER A 387 1 6
HELIX 18 AB9 PHE A 399 GLY A 412 1 14
HELIX 19 AC1 PHE A 414 ASN A 432 1 19
HELIX 20 AC2 LYS A 436 SER A 450 1 15
HELIX 21 AC3 ASN A 459 ASN A 486 1 28
HELIX 22 AC4 GLY B 87 GLU B 104 1 18
HELIX 23 AC5 SER B 117 LEU B 129 1 13
HELIX 24 AC6 ASP B 137 SER B 139 5 3
HELIX 25 AC7 VAL B 140 ASN B 150 1 11
HELIX 26 AC8 GLY B 161 SER B 171 1 11
HELIX 27 AC9 ASP B 182 ASN B 196 1 15
HELIX 28 AD1 ASN B 204 HIS B 222 1 19
HELIX 29 AD2 ASP B 231 CYS B 240 1 10
HELIX 30 AD3 ASP B 242 LEU B 247 1 6
HELIX 31 AD4 ASN B 255 ASN B 260 1 6
HELIX 32 AD5 THR B 278 VAL B 285 1 8
HELIX 33 AD6 THR B 286 LYS B 292 1 7
HELIX 34 AD7 GLY B 299 MET B 309 1 11
HELIX 35 AD8 MET B 309 ASP B 324 1 16
HELIX 36 AD9 ASP B 326 ASN B 328 5 3
HELIX 37 AE1 MET B 360 TRP B 370 1 11
HELIX 38 AE2 ASP B 382 SER B 387 1 6
HELIX 39 AE3 PHE B 399 GLY B 412 1 14
HELIX 40 AE4 PHE B 414 ASN B 432 1 19
HELIX 41 AE5 LYS B 436 PHE B 451 1 16
HELIX 42 AE6 ASN B 459 ASN B 486 1 28
SHEET 1 AA1 7 ILE A 157 CYS A 160 0
SHEET 2 AA1 7 TYR A 132 ILE A 135 1 N LEU A 133 O LEU A 159
SHEET 3 AA1 7 PHE A 107 VAL A 114 1 N LYS A 110 O TYR A 132
SHEET 4 AA1 7 ILE A 78 PHE A 83 1 N ILE A 78 O ASN A 108
SHEET 5 AA1 7 LYS A 176 ILE A 179 1 O VAL A 178 N ALA A 81
SHEET 6 AA1 7 ILE A 199 LEU A 202 1 O ALA A 201 N ILE A 179
SHEET 7 AA1 7 LYS A 226 PRO A 229 1 O LYS A 226 N VAL A 200
SHEET 1 AA2 8 ILE A 330 VAL A 334 0
SHEET 2 AA2 8 ILE A 262 SER A 269 1 N LEU A 267 O GLU A 331
SHEET 3 AA2 8 ILE A 340 PHE A 346 -1 O GLU A 345 N LYS A 264
SHEET 4 AA2 8 VAL A 351 MET A 355 -1 O ILE A 352 N VAL A 344
SHEET 5 AA2 8 VAL B 351 MET B 355 -1 O MET B 355 N VAL A 351
SHEET 6 AA2 8 ILE B 340 PHE B 346 -1 N VAL B 344 O ILE B 352
SHEET 7 AA2 8 ILE B 262 SER B 269 -1 N LYS B 264 O GLU B 345
SHEET 8 AA2 8 ILE B 330 VAL B 334 1 O GLU B 331 N LEU B 267
SHEET 1 AA3 2 THR A 388 THR A 390 0
SHEET 2 AA3 2 THR B 388 THR B 390 -1 O LEU B 389 N LEU A 389
SHEET 1 AA4 7 ILE B 157 CYS B 160 0
SHEET 2 AA4 7 TYR B 132 ILE B 135 1 N LEU B 133 O LEU B 159
SHEET 3 AA4 7 PHE B 107 VAL B 114 1 N LYS B 110 O TYR B 132
SHEET 4 AA4 7 ILE B 78 PHE B 83 1 N ILE B 78 O ASN B 108
SHEET 5 AA4 7 LYS B 176 ILE B 179 1 O VAL B 178 N ALA B 81
SHEET 6 AA4 7 ILE B 199 LEU B 202 1 O ALA B 201 N ILE B 179
SHEET 7 AA4 7 LYS B 226 PRO B 229 1 O LYS B 226 N VAL B 200
LINK OD1 ASP A 231 MN MN A 502 1555 1555 2.13
LINK OE1 GLU A 233 MN MN A 502 1555 1555 2.10
LINK OE2 GLU A 315 MN MN A 502 1555 1555 2.07
LINK O12 RC5 A 501 MN MN A 502 1555 1555 2.16
LINK O10 RC5 A 501 MN MN A 502 1555 1555 2.14
LINK OD1 ASP B 231 MN MN B 502 1555 1555 2.11
LINK OE1 GLU B 233 MN MN B 502 1555 1555 2.10
LINK OE2 GLU B 315 MN MN B 502 1555 1555 2.08
LINK O12 RC5 B 501 MN MN B 502 1555 1555 2.14
LINK O10 RC5 B 501 MN MN B 502 1555 1555 2.15
CISPEP 1 TRP A 370 PRO A 371 0 5.93
CISPEP 2 TRP B 370 PRO B 371 0 5.91
SITE 1 AC1 17 LYS A 205 ASP A 231 SER A 232 GLU A 233
SITE 2 AC1 17 SER A 269 SER A 270 TRP A 296 SER A 306
SITE 3 AC1 17 ASN A 311 LYS A 312 GLU A 315 HIS A 341
SITE 4 AC1 17 ASP A 359 MN A 502 HOH A 705 HOH A 728
SITE 5 AC1 17 HOH A 805
SITE 1 AC2 5 LYS A 205 ASP A 231 GLU A 233 GLU A 315
SITE 2 AC2 5 RC5 A 501
SITE 1 AC3 17 LYS B 205 ASP B 231 SER B 232 GLU B 233
SITE 2 AC3 17 SER B 269 SER B 270 TRP B 296 SER B 306
SITE 3 AC3 17 ASN B 311 LYS B 312 GLU B 315 HIS B 341
SITE 4 AC3 17 ASP B 359 MN B 502 HOH B 697 HOH B 716
SITE 5 AC3 17 HOH B 719
SITE 1 AC4 5 LYS B 205 ASP B 231 GLU B 233 GLU B 315
SITE 2 AC4 5 RC5 B 501
CRYST1 51.570 56.465 86.024 104.11 103.25 100.16 P 1 2
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 0.019391 0.003474 0.005860 0.00000
SCALE2 0.000000 0.017992 0.005588 0.00000
SCALE3 0.000000 0.000000 0.012505 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
