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PDBsum entry 3rye

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Transferase PDB id
3rye
Jmol
Contents
Protein chain
341 a.a.
Ligands
UNR
SO4
Metals
_MG ×3
Waters ×151
HEADER    TRANSFERASE                             11-MAY-11   3RYE
TITLE     HUMAN FDPS SYNTHASE IN COMPLEX WITH A N-METHYL PYRIDINUM
TITLE    2 BISPHOSPHONATE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: FPP SYNTHASE, FPS, (2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE,
COMPND   5 DIMETHYLALLYLTRANSTRANSFERASE, FARNESYL DIPHOSPHATE SYNTHASE,
COMPND   6 GERANYLTRANSTRANSFERASE;
COMPND   7 EC: 2.5.1.10, 2.5.1.1;
COMPND   8 ENGINEERED: YES;
COMPND   9 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: FDPS, FPS, KIAA1293;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: P11
KEYWDS    MAINLY ALPHA HELIX, ISOPRENE, LIPID, STEROID BIOSYNTHESIS, MAGNESIUM
KEYWDS   2 BINDING, TRANSFERASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    A.G.EVDOKIMOV,B.L.BARNETT,F.H.EBETINO,M.POKROSS
REVDAT   1   01-JUN-11 3RYE    0
JRNL        AUTH   A.G.EVDOKIMOV,B.L.BARNETT,F.H.EBETINO,M.POKROSS
JRNL        TITL   HUMAN FDPS SYNTHASE IN COMPLEX WITH A N-METHYL PYRIDINUM
JRNL        TITL 2 BISPHOSPHONATE
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    2.10 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.5.0109
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.20
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.4
REMARK   3   NUMBER OF REFLECTIONS             : 23382
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) : 0.185
REMARK   3   R VALUE            (WORKING SET) : 0.185
REMARK   3   FREE R VALUE                     : 0.239
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 1262
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) : 2.10
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.15
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1321
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 73.26
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2240
REMARK   3   BIN FREE R VALUE SET COUNT          : 60
REMARK   3   BIN FREE R VALUE                    : 0.2460
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2762
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 26
REMARK   3   SOLVENT ATOMS            : 151
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 44.90
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 44.92
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.29000
REMARK   3    B22 (A**2) : -0.29000
REMARK   3    B33 (A**2) : 0.57000
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): NULL
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.184
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): NULL
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.965
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2842 ; 0.022 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3854 ; 1.980 ; 1.978
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   339 ; 5.000 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   141 ;24.750 ;24.752
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   496 ;15.000 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    15 ;15.000 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   420 ; 0.200 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2153 ; 0.021 ; 0.021
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
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):  1697 ; 2.016 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2730 ; 3.185 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1145 ; 5.142 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1124 ; 7.956 ; 4.500
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  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
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 3RYE COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-11.
REMARK 100 THE RCSB ID CODE IS RCSB065530.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 03-MAY-05
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 4.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
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) : 1.0
REMARK 200  MONOCHROMATOR                  : SI
REMARK 200  OPTICS                         : MIRROR/SLIT
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : MARMOSAIC 325 MM CCD
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 23382
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.100
REMARK 200  RESOLUTION RANGE LOW       (A) : 35.200
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.4
REMARK 200  DATA REDUNDANCY                : 4.300
REMARK 200  R MERGE                    (I) : 0.04000
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 16.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.20
REMARK 200  COMPLETENESS FOR SHELL     (%) : 65.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.80
REMARK 200  R MERGE FOR SHELL          (I) : 0.20000
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 5.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 2VF6
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 54.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 15%
REMARK 280  ISOPROPANOL, 15% ETHYLENE GLYCOL, PH 4.5, VAPOR DIFFUSION,
REMARK 280  HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
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       34.85650
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       55.65550
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       55.65550
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       17.42825
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       55.65550
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       55.65550
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       52.28475
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       55.65550
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       55.65550
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       17.42825
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       55.65550
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       55.65550
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       52.28475
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       34.85650
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: 5090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27760 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 350   BIOMT1   2  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT2   2 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       34.85650
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     SER A     5
REMARK 465     ASN A     6
REMARK 465     SER A     7
REMARK 465     MET A    33
REMARK 465     GLY A    34
REMARK 465     ARG A   351
REMARK 465     ARG A   352
REMARK 465     LYS A   353
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   OD2  ASP A   184     CG1  VAL A   186              1.98
REMARK 500   OE2  GLU A    13     NH1  ARG A    69              1.99
REMARK 500   O    HOH A   428     O    HOH A   478              2.02
REMARK 500   O    HOH A   447     O    HOH A   468              2.12
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   395     O    HOH A   395     8555     1.69
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    GLN A  77       51.09    -93.04
REMARK 500    VAL A 124      -72.38    -96.97
REMARK 500    VAL A 183      -93.85    -50.04
REMARK 500    PHE A 206      -54.59   -124.56
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 ASP A    8     VAL A    9                 -144.62
REMARK 500 VAL A  183     ASP A  184                 -109.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    ASP A 184        25.0      L          L   OUTSIDE RANGE
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                              MG A 909  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A   3   O
REMARK 620 2 ASP A 103   OD2 178.5
REMARK 620 3 HOH A 433   O    86.7  92.6
REMARK 620 4 HOH A 501   O    93.9  87.5  96.2
REMARK 620 5 ASP A 107   OD2  95.5  83.2  94.0 166.5
REMARK 620 6 UNR A 901   O5   89.6  91.0 174.0  88.7  81.7
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 908  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 UNR A 901   O8
REMARK 620 2 UNR A 901   O6   84.4
REMARK 620 3 HOH A 476   O    94.7  92.4
REMARK 620 4 HOH A 496   O   178.7  94.3  85.5
REMARK 620 5 HOH A 499   O    91.4 175.7  87.6  89.9
REMARK 620 6 ASP A 243   OD2  89.9  94.4 172.1  90.0  85.9
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 907  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 500   O
REMARK 620 2 UNR A 901   O9   90.9
REMARK 620 3 UNR A 901   O5  102.5  90.6
REMARK 620 4 ASP A 103   OD1 161.3  95.1  95.2
REMARK 620 5 HOH A 497   O    83.2  87.9 174.1  79.3
REMARK 620 6 ASP A 107   OD2  90.1 172.8  82.3  86.1  99.3
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 UNR A 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 907
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 908
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 909
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1YV5   RELATED DB: PDB
REMARK 900 FDPS WITH RISEDRONATE
REMARK 900 RELATED ID: 2RAH   RELATED DB: PDB
REMARK 900 FDPS WITH NOVEL INHIBITOR
REMARK 900 RELATED ID: 2VF6   RELATED DB: PDB
REMARK 900 FDPS WITH MINODRONATE
DBREF  3RYE A    5   353  UNP    P14324   FPPS_HUMAN      71    419
SEQADV 3RYE SER A    5  UNP  P14324    GLN    71 ENGINEERED MUTATION
SEQRES   1 A  349  SER ASN SER ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE
SEQRES   2 A  349  VAL GLN HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU
SEQRES   3 A  349  ASP GLU MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA
SEQRES   4 A  349  ARG LEU LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY
SEQRES   5 A  349  LYS TYR ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG
SEQRES   6 A  349  GLU LEU VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU
SEQRES   7 A  349  GLN ARG ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU
SEQRES   8 A  349  GLN ALA PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER
SEQRES   9 A  349  SER LEU THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS
SEQRES  10 A  349  PRO GLY VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU
SEQRES  11 A  349  LEU GLU ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS
SEQRES  12 A  349  ARG GLU GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE
SEQRES  13 A  349  LEU GLN SER SER TYR GLN THR GLU ILE GLY GLN THR LEU
SEQRES  14 A  349  ASP LEU LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL
SEQRES  15 A  349  ARG PHE THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR
SEQRES  16 A  349  LYS THR ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA
SEQRES  17 A  349  ALA MET TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS
SEQRES  18 A  349  ALA ASN ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE
SEQRES  19 A  349  PHE GLN ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP
SEQRES  20 A  349  PRO SER VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP
SEQRES  21 A  349  ASN LYS CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG
SEQRES  22 A  349  ALA THR PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR
SEQRES  23 A  349  GLY GLN LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA
SEQRES  24 A  349  LEU TYR GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN
SEQRES  25 A  349  TYR GLU GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE
SEQRES  26 A  349  GLU GLN TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU
SEQRES  27 A  349  GLY LEU ALA ARG LYS ILE TYR LYS ARG ARG LYS
HET    UNR  A 901      18
HET     MG  A 907       1
HET     MG  A 908       1
HET     MG  A 909       1
HET    SO4  A1001       5
HETNAM     UNR 3-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-1-METHYLPYRIDINIUM
HETNAM      MG MAGNESIUM ION
HETNAM     SO4 SULFATE ION
FORMUL   2  UNR    C8 H14 N O7 P2 1+
FORMUL   3   MG    3(MG 2+)
FORMUL   6  SO4    O4 S 2-
FORMUL   7  HOH   *151(H2 O)
HELIX    1   1 GLU A   13  HIS A   20  1                                   8
HELIX    2   2 HIS A   20  LEU A   28  1                                   9
HELIX    3   3 HIS A   35  GLU A   37  5                                   3
HELIX    4   4 ILE A   38  ALA A   53  1                                  16
HELIX    5   5 TYR A   58  VAL A   72  1                                  15
HELIX    6   6 GLU A   73  GLN A   77  5                                   5
HELIX    7   7 ASP A   78  ASP A  107  1                                  30
HELIX    8   8 TRP A  118  LYS A  121  5                                   4
HELIX    9   9 VAL A  124  LEU A  126  5                                   3
HELIX   10  10 ASP A  127  ARG A  148  1                                  22
HELIX   11  11 TYR A  152  ALA A  178  1                                  27
HELIX   12  12 ASP A  184  PHE A  188  5                                   5
HELIX   13  13 THR A  189  THR A  201  1                                  13
HELIX   14  14 THR A  201  PHE A  206  1                                   6
HELIX   15  15 PHE A  206  ALA A  217  1                                  12
HELIX   16  16 GLY A  221  GLY A  250  1                                  30
HELIX   17  17 ASP A  251  GLY A  256  1                                   6
HELIX   18  18 SER A  268  ALA A  278  1                                  11
HELIX   19  19 THR A  279  TYR A  290  1                                  12
HELIX   20  20 GLU A  294  LEU A  308  1                                  15
HELIX   21  21 ASP A  309  ALA A  333  1                                  25
HELIX   22  22 PRO A  337  LYS A  350  1                                  14
SHEET    1   A 2 THR A 111  ARG A 112  0
SHEET    2   A 2 GLN A 115  ILE A 116 -1  O  GLN A 115   N  ARG A 112
LINK        MG    MG A 909                 O   HOH A   3     1555   1555  1.96
LINK         O8  UNR A 901                MG    MG A 908     1555   1555  1.97
LINK         O6  UNR A 901                MG    MG A 908     1555   1555  2.01
LINK        MG    MG A 908                 O   HOH A 476     1555   1555  2.02
LINK        MG    MG A 907                 O   HOH A 500     1555   1555  2.02
LINK         OD2 ASP A 103                MG    MG A 909     1555   1555  2.03
LINK         O9  UNR A 901                MG    MG A 907     1555   1555  2.03
LINK         O5  UNR A 901                MG    MG A 907     1555   1555  2.07
LINK        MG    MG A 908                 O   HOH A 496     1555   1555  2.07
LINK        MG    MG A 909                 O   HOH A 433     1555   1555  2.07
LINK        MG    MG A 909                 O   HOH A 501     1555   1555  2.08
LINK         OD1 ASP A 103                MG    MG A 907     1555   1555  2.09
LINK         OD2 ASP A 107                MG    MG A 909     1555   1555  2.11
LINK        MG    MG A 907                 O   HOH A 497     1555   1555  2.12
LINK         O5  UNR A 901                MG    MG A 909     1555   1555  2.19
LINK         OD2 ASP A 107                MG    MG A 907     1555   1555  2.21
LINK        MG    MG A 908                 O   HOH A 499     1555   1555  2.23
LINK         OD2 ASP A 243                MG    MG A 908     1555   1555  2.26
CISPEP   1 ALA A  334    PRO A  335          0        11.45
SITE     1 AC1 21 HOH A   3  ASP A 103  ASP A 107  ARG A 112
SITE     2 AC1 21 GLN A 171  LYS A 200  THR A 201  ASP A 243
SITE     3 AC1 21 LYS A 257  HOH A 373  HOH A 416  HOH A 417
SITE     4 AC1 21 HOH A 476  HOH A 496  HOH A 497  HOH A 499
SITE     5 AC1 21 HOH A 500  HOH A 501   MG A 907   MG A 908
SITE     6 AC1 21  MG A 909
SITE     1 AC2  6 ASP A 103  ASP A 107  HOH A 497  HOH A 500
SITE     2 AC2  6 UNR A 901   MG A 909
SITE     1 AC3  5 ASP A 243  HOH A 476  HOH A 496  HOH A 499
SITE     2 AC3  5 UNR A 901
SITE     1 AC4  7 HOH A   3  ASP A 103  ASP A 107  HOH A 433
SITE     2 AC4  7 HOH A 501  UNR A 901   MG A 907
SITE     1 AC5  7 HOH A   4  GLY A  56  LYS A  57  GLN A  96
SITE     2 AC5  7 ARG A 113  HOH A 354  HOH A 370
CRYST1  111.311  111.311   69.713  90.00  90.00  90.00 P 41 21 2     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      0.008984  0.000000  0.000000        0.00000
SCALE2      0.000000  0.008984  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014345        0.00000
      
PROCHECK
Go to PROCHECK summary
 References