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PDBsum entry 2vk6

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Hydrolase PDB id
2vk6
Jmol
Contents
Protein chain
449 a.a.
Ligands
DAN
PG4
Metals
_CA
_MG ×4
Waters ×396
HEADER    HYDROLASE                               17-DEC-07   2VK6
TITLE     THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND
TITLE    2 ITS CATALYTIC INTERMEDIATES
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: EXO-ALPHA-SIALIDASE;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 243-694;
COMPND   5 SYNONYM: SIALIDASE;
COMPND   6 EC: 3.2.1.18;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS;
SOURCE   3 ORGANISM_TAXID: 1502;
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    HYDROLASE, SIALIDASE, GLYCOSIDASE, SIALIC ACID, CLOSTRIDIUM
KEYWDS   2 PERFRINGENS
EXPDTA    X-RAY DIFFRACTION
AUTHOR    S.L.NEWSTEAD,J.A.POTTER,J.C.WILSON,G.XU,C.H.CHIEN,A.G.WATTS,
AUTHOR   2 S.G.WITHERS,G.L.TAYLOR
REVDAT   3   24-FEB-09 2VK6    1       VERSN
REVDAT   2   08-APR-08 2VK6    1       JRNL   REMARK
REVDAT   1   22-JAN-08 2VK6    0
JRNL        AUTH   S.L.NEWSTEAD,J.A.POTTER,J.C.WILSON,G.XU,C.H.CHIEN,
JRNL        AUTH 2 A.G.WATTS,S.G.WITHERS,G.L.TAYLOR
JRNL        TITL   THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI
JRNL        TITL 2 SIALIDASE AND ITS CATALYTIC INTERMEDIATES.
JRNL        REF    J.BIOL.CHEM.                  V. 283  9080 2008
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   18218621
JRNL        DOI    10.1074/JBC.M710247200
REMARK   2
REMARK   2 RESOLUTION.    1.50 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0005
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) : 1.50
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 28.40
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 92.8
REMARK   3   NUMBER OF REFLECTIONS             : 69514
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) : 0.161
REMARK   3   R VALUE            (WORKING SET) : 0.160
REMARK   3   FREE R VALUE                     : 0.185
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 3675
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) : 1.50
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.54
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 4895
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2060
REMARK   3   BIN FREE R VALUE SET COUNT          : 243
REMARK   3   BIN FREE R VALUE                    : 0.2740
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3657
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 38
REMARK   3   SOLVENT ATOMS            : 396
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 13.11
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  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): NULL
REMARK   3   ESU BASED ON FREE R VALUE                       (A): NULL
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 : 0.956
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3778 ; 0.018 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5136 ; 1.713 ; 1.965
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   477 ; 7.061 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   188 ;36.546 ;25.745
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   664 ;11.941 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    15 ;12.044 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   556 ; 0.134 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2911 ; 0.010 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1701 ; 0.203 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2609 ; 0.310 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   342 ; 0.121 ; 0.200
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):    43 ; 0.115 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    19 ; 0.128 ; 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):  2352 ; 1.136 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3721 ; 1.700 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1639 ; 2.598 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1402 ; 3.614 ; 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   : 1.20
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
REMARK   3  RIDING POSITIONS.
REMARK   4
REMARK   4 2VK6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-07.
REMARK 100 THE PDBE ID CODE IS EBI-34808.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
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               : ESRF
REMARK 200  BEAMLINE                       : ID14-2
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.934
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 73189
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.50
REMARK 200  RESOLUTION RANGE LOW       (A) : 28.40
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 93.0
REMARK 200  DATA REDUNDANCY                : 3.4
REMARK 200  R MERGE                    (I) : 0.06
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 15.50
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.54
REMARK 200  COMPLETENESS FOR SHELL     (%) : 89.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.1
REMARK 200  R MERGE FOR SHELL          (I) : 0.29
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 3.60
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: NULL
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 49.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):2.33
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
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       34.68500
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       49.45000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       35.52300
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       49.45000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       34.68500
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       35.52300
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 GENERATING THE BIOMOLECULE
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PQS
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 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  1692
REMARK 465     ASN A  1693
REMARK 465     LYS A  1694
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     GLY A1691    CA   C    O
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 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    ILE A1267       76.78     76.86
REMARK 500    ASN A1294       46.42    -87.41
REMARK 500    ASP A1328       95.36     77.54
REMARK 500    LYS A1350       -5.10     85.83
REMARK 500    ASP A1414     -158.07   -172.31
REMARK 500    LYS A1459      -70.16    -93.60
REMARK 500    THR A1538     -122.73   -123.08
REMARK 500    TYR A1587       61.59     76.06
REMARK 500    ALA A1654     -113.76   -124.20
REMARK 500    SER A1675       29.45   -157.45
REMARK 500    GLU A1676      -95.95   -123.08
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 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                              CA A2691  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2096   O
REMARK 620 2 ASP A1298   OD1  69.9
REMARK 620 3 ASP A1319   OD1 106.1  81.7
REMARK 620 4 TYR A1320   O    73.9 133.1  80.7
REMARK 620 5 HOH A2068   O   141.3 148.2  91.1  75.1
REMARK 620 6 HOH A2070   O   141.4  76.1  86.2 144.7  72.5
REMARK 620 7 ASP A1296   OD1  82.4 101.9 171.5 101.8  81.7  87.2
REMARK 620 N                    1     2     3     4     5     6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A2693  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2163   O
REMARK 620 2 HOH A2170   O   110.4
REMARK 620 3 HOH A2387   O   131.3 115.6
REMARK 620 N                    1     2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A2694  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 TRP A1573   O
REMARK 620 2 HOH A2237   O    88.1
REMARK 620 3 HOH A2239   O    82.6 101.1
REMARK 620 4 HOH A2236   O   106.2  78.5 171.1
REMARK 620 5 HOH A2241   O    89.2 165.5  92.6  88.7
REMARK 620 6 ASP A1515   O   167.9  87.2  87.4  83.7  98.1
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A2695  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2076   O
REMARK 620 2 HOH A2075   O   107.9
REMARK 620 3 HOH A2384   O   111.5 123.3
REMARK 620 N                    1     2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A2696  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2095   O
REMARK 620 2 HOH A2033   O   104.4
REMARK 620 3 HOH A2167   O   110.9 114.9
REMARK 620 4 HOH A2251   O   105.6  96.4 122.3
REMARK 620 N                    1     2     3
REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS ARE DEFINED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  CA A2691
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAN A2692
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  MG A2693
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  MG A2694
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  MG A2695
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  MG A2696
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A2697
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2BF6   RELATED DB: PDB
REMARK 900  ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL
REMARK 900  SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN
REMARK 900   COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).
REMARK 900 RELATED ID: 2VK5   RELATED DB: PDB
REMARK 900  THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI
REMARK 900   SIALIDASE AND ITS CATALYTIC INTERMEDIATES
REMARK 900 RELATED ID: 2VK7   RELATED DB: PDB
REMARK 900  THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI
REMARK 900   SIALIDASE AND ITS CATALYTIC INTERMEDIATE
DBREF  2VK6 A 1243  1694  UNP    Q59310   Q59310_CLOPE   243    694
SEQADV 2VK6 SER A 1393  UNP  Q59310    GLY   393 CONFLICT
SEQRES   1 A  452  VAL GLU GLY ALA VAL LYS THR GLU PRO VAL ASP LEU PHE
SEQRES   2 A  452  HIS PRO GLY PHE LEU ASN SER SER ASN TYR ARG ILE PRO
SEQRES   3 A  452  ALA LEU PHE LYS THR LYS GLU GLY THR LEU ILE ALA SER
SEQRES   4 A  452  ILE ASP ALA ARG ARG HIS GLY GLY ALA ASP ALA PRO ASN
SEQRES   5 A  452  ASN ASP ILE ASP THR ALA VAL ARG ARG SER GLU ASP GLY
SEQRES   6 A  452  GLY LYS THR TRP ASP GLU GLY GLN ILE ILE MET ASP TYR
SEQRES   7 A  452  PRO ASP LYS SER SER VAL ILE ASP THR THR LEU ILE GLN
SEQRES   8 A  452  ASP ASP GLU THR GLY ARG ILE PHE LEU LEU VAL THR HIS
SEQRES   9 A  452  PHE PRO SER LYS TYR GLY PHE TRP ASN ALA GLY LEU GLY
SEQRES  10 A  452  SER GLY PHE LYS ASN ILE ASP GLY LYS GLU TYR LEU CYS
SEQRES  11 A  452  LEU TYR ASP SER SER GLY LYS GLU PHE THR VAL ARG GLU
SEQRES  12 A  452  ASN VAL VAL TYR ASP LYS ASP SER ASN LYS THR GLU TYR
SEQRES  13 A  452  THR THR ASN ALA LEU GLY ASP LEU PHE LYS ASN GLY THR
SEQRES  14 A  452  LYS ILE ASP ASN ILE ASN SER SER THR ALA PRO LEU LYS
SEQRES  15 A  452  ALA LYS GLY THR SER TYR ILE ASN LEU VAL TYR SER ASP
SEQRES  16 A  452  ASP ASP GLY LYS THR TRP SER GLU PRO GLN ASN ILE ASN
SEQRES  17 A  452  PHE GLN VAL LYS LYS ASP TRP MET LYS PHE LEU GLY ILE
SEQRES  18 A  452  ALA PRO GLY ARG GLY ILE GLN ILE LYS ASN GLY GLU HIS
SEQRES  19 A  452  LYS GLY ARG ILE VAL VAL PRO VAL TYR TYR THR ASN GLU
SEQRES  20 A  452  LYS GLY LYS GLN SER SER ALA VAL ILE TYR SER ASP ASP
SEQRES  21 A  452  SER GLY LYS ASN TRP THR ILE GLY GLU SER PRO ASN ASP
SEQRES  22 A  452  ASN ARG LYS LEU GLU ASN GLY LYS ILE ILE ASN SER LYS
SEQRES  23 A  452  THR LEU SER ASP ASP ALA PRO GLN LEU THR GLU CYS GLN
SEQRES  24 A  452  VAL VAL GLU MET PRO ASN GLY GLN LEU LYS LEU PHE MET
SEQRES  25 A  452  ARG ASN LEU SER GLY TYR LEU ASN ILE ALA THR SER PHE
SEQRES  26 A  452  ASP GLY GLY ALA THR TRP ASP GLU THR VAL GLU LYS ASP
SEQRES  27 A  452  THR ASN VAL LEU GLU PRO TYR CYS GLN LEU SER VAL ILE
SEQRES  28 A  452  ASN TYR SER GLN LYS VAL ASP GLY LYS ASP ALA VAL ILE
SEQRES  29 A  452  PHE SER ASN PRO ASN ALA ARG SER ARG SER ASN GLY THR
SEQRES  30 A  452  VAL ARG ILE GLY LEU ILE ASN GLN VAL GLY THR TYR GLU
SEQRES  31 A  452  ASN GLY GLU PRO LYS TYR GLU PHE ASP TRP LYS TYR ASN
SEQRES  32 A  452  LYS LEU VAL LYS PRO GLY TYR TYR ALA TYR SER CYS LEU
SEQRES  33 A  452  THR GLU LEU SER ASN GLY ASN ILE GLY LEU LEU TYR GLU
SEQRES  34 A  452  GLY THR PRO SER GLU GLU MET SER TYR ILE GLU MET ASN
SEQRES  35 A  452  LEU LYS TYR LEU GLU SER GLY ALA ASN LYS
HET     CA  A2691       1
HET    DAN  A2692      20
HET     MG  A2693       1
HET     MG  A2694       1
HET     MG  A2695       1
HET     MG  A2696       1
HET    PG4  A2697      13
HETNAM     PG4 TETRAETHYLENE GLYCOL
HETNAM      CA CALCIUM ION
HETNAM      MG MAGNESIUM ION
HETNAM     DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
FORMUL   2  PG4    C8 H18 O5
FORMUL   3   CA    CA 2+
FORMUL   4   MG    4(MG 2+)
FORMUL   5  DAN    C11 H17 N O8
FORMUL   6  HOH   *396(H2 O1)
HELIX    1   1 GLY A 1258  SER A 1262  5                                   5
HELIX    2   2 ILE A 1449  LYS A 1454  1                                   6
HELIX    3   3 ASN A 1684  GLU A 1689  1                                   6
SHEET    1  AA 4 VAL A1252  PHE A1255  0
SHEET    2  AA 4 MET A1678  MET A1683 -1  O  MET A1678   N  LEU A1254
SHEET    3  AA 4 ILE A1666  GLU A1671 -1  O  ILE A1666   N  MET A1683
SHEET    4  AA 4 SER A1656  GLU A1660 -1  O  CYS A1657   N  LEU A1669
SHEET    1  AB 4 ASN A1264  LYS A1272  0
SHEET    2  AB 4 LEU A1278  ARG A1285 -1  O  ILE A1279   N  PHE A1271
SHEET    3  AB 4 ILE A1297  SER A1304 -1  O  ASP A1298   N  ALA A1284
SHEET    4  AB 4 GLN A1315  MET A1318 -1  O  GLN A1315   N  VAL A1301
SHEET    1  AC 5 GLN A1447  ASN A1448  0
SHEET    2  AC 5 TYR A1430  SER A1436 -1  O  LEU A1433   N  GLN A1447
SHEET    3  AC 5 ILE A1340  PHE A1347 -1  O  ILE A1340   N  SER A1436
SHEET    4  AC 5 SER A1325  GLN A1333 -1  O  SER A1325   N  PHE A1347
SHEET    5  AC 5 GLY A1466  ARG A1467  1  O  GLY A1466   N  LEU A1331
SHEET    1  AD 7 PHE A1362  ILE A1365  0
SHEET    2  AD 7 LYS A1368  TYR A1374 -1  O  LYS A1368   N  ILE A1365
SHEET    3  AD 7 GLU A1380  ARG A1384 -1  O  PHE A1381   N  LEU A1373
SHEET    4  AD 7 VAL A1387  TYR A1389 -1  O  VAL A1387   N  ARG A1384
SHEET    5  AD 7 LYS A1395  THR A1400 -1  N  THR A1396   O  VAL A1388
SHEET    6  AD 7 ASP A1405  LYS A1408 -1  O  PHE A1407   N  THR A1399
SHEET    7  AD 7 THR A1411  ASN A1415 -1  O  THR A1411   N  LYS A1408
SHEET    1  AE 3 PHE A1362  ILE A1365  0
SHEET    2  AE 3 LYS A1368  TYR A1374 -1  O  LYS A1368   N  ILE A1365
SHEET    3  AE 3 LYS A1424  ALA A1425 -1  O  LYS A1424   N  TYR A1374
SHEET    1  AF 3 LEU A1461  ILE A1463  0
SHEET    2  AF 3 ILE A1480  THR A1487 -1  O  TYR A1485   N  GLY A1462
SHEET    3  AF 3 ILE A1469  GLN A1470 -1  O  ILE A1469   N  VAL A1481
SHEET    1  AG 4 LEU A1461  ILE A1463  0
SHEET    2  AG 4 ILE A1480  THR A1487 -1  O  TYR A1485   N  GLY A1462
SHEET    3  AG 4 GLN A1493  SER A1500 -1  O  SER A1494   N  TYR A1486
SHEET    4  AG 4 THR A1508  ILE A1509 -1  O  THR A1508   N  TYR A1499
SHEET    1  AH 2 ARG A1517  LYS A1518  0
SHEET    2  AH 2 ILE A1524  ILE A1525 -1  N  ILE A1525   O  ARG A1517
SHEET    1  AI 4 LEU A1537  GLU A1544  0
SHEET    2  AI 4 LEU A1550  ASN A1556 -1  O  LYS A1551   N  VAL A1543
SHEET    3  AI 4 TYR A1560  SER A1566 -1  O  ASN A1562   N  MET A1554
SHEET    4  AI 4 GLU A1578  LEU A1584 -1  O  GLU A1578   N  ILE A1563
SHEET    1  AJ 4 SER A1591  ASN A1594  0
SHEET    2  AJ 4 ALA A1604  PRO A1610 -1  O  ILE A1606   N  ILE A1593
SHEET    3  AJ 4 SER A1616  THR A1630 -1  O  THR A1619   N  ASN A1609
SHEET    4  AJ 4 PRO A1636  TYR A1652 -1  O  LYS A1637   N  VAL A1628
LINK        CA    CA A2691                 O   HOH A2096     1555   1555  2.54
LINK        CA    CA A2691                 OD1 ASP A1298     1555   1555  2.45
LINK        CA    CA A2691                 OD1 ASP A1319     1555   1555  2.39
LINK        CA    CA A2691                 O   TYR A1320     1555   1555  2.36
LINK        CA    CA A2691                 O   HOH A2068     1555   1555  2.48
LINK        CA    CA A2691                 O   HOH A2070     1555   1555  2.47
LINK        CA    CA A2691                 OD1 ASP A1296     1555   1555  2.35
LINK        MG    MG A2693                 O   HOH A2163     1555   1555  2.28
LINK        MG    MG A2693                 O   HOH A2170     1555   1555  2.67
LINK        MG    MG A2693                 O   HOH A2387     1555   1555  2.75
LINK        MG    MG A2694                 O   HOH A2236     1555   1555  2.64
LINK        MG    MG A2694                 O   HOH A2237     1555   1555  2.54
LINK        MG    MG A2694                 O   HOH A2239     1555   1555  2.37
LINK        MG    MG A2694                 O   HOH A2241     1555   1555  2.35
LINK        MG    MG A2694                 O   ASP A1515     1555   1555  2.36
LINK        MG    MG A2694                 O   TRP A1573     1555   1555  2.50
LINK        MG    MG A2695                 O   HOH A2075     1555   1555  2.65
LINK        MG    MG A2695                 O   HOH A2384     1555   1555  2.76
LINK        MG    MG A2695                 O   HOH A2076     1555   1555  2.77
LINK        MG    MG A2696                 O   HOH A2033     1555   2565  2.84
LINK        MG    MG A2696                 O   HOH A2167     1555   1555  2.74
LINK        MG    MG A2696                 O   HOH A2251     1555   2565  2.74
LINK        MG    MG A2696                 O   HOH A2095     1555   1555  2.68
CISPEP   1 ALA A 1292    PRO A 1293          0         7.40
SITE     1 AC1  7 ASP A1296  ASP A1298  ASP A1319  TYR A1320
SITE     2 AC1  7 HOH A2068  HOH A2070  HOH A2096
SITE     1 AC2 17 ARG A1266  ILE A1267  ARG A1285  ASP A1291
SITE     2 AC2 17 ILE A1327  ASP A1328  PHE A1353  TYR A1485
SITE     3 AC2 17 GLN A1493  ARG A1555  TYR A1587  ARG A1615
SITE     4 AC2 17 TYR A1655  HOH A2263  HOH A2298  HOH A2392
SITE     5 AC2 17 HOH A2393
SITE     1 AC3  4 ASP A1322  HOH A2163  HOH A2170  HOH A2387
SITE     1 AC4  6 ASP A1515  TRP A1573  HOH A2236  HOH A2237
SITE     2 AC4  6 HOH A2239  HOH A2241
SITE     1 AC5  4 VAL A1252  HOH A2075  HOH A2076  HOH A2384
SITE     1 AC6  5 ILE A1524  HOH A2033  HOH A2095  HOH A2167
SITE     2 AC6  5 HOH A2251
SITE     1 AC7  6 ASP A1312  GLY A1314  GLN A1315  TRP A1354
SITE     2 AC7  6 HOH A2079  HOH A2395
CRYST1   69.370   71.046   98.900  90.00  90.00  90.00 P 21 21 21    4
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      0.014415  0.000000  0.000000        0.00000
SCALE2      0.000000  0.014075  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010111        0.00000
      
PROCHECK
Go to PROCHECK summary
 References