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PDBsum entry 2jkb

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Lyase PDB id
2jkb
Jmol
Contents
Protein chain
661 a.a.
Ligands
SKD
EDO ×6
Waters ×1024
HEADER    LYASE                                   26-AUG-08   2JKB
TITLE     CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANB IN
TITLE    2 COMPLEX WITH 2,7-ANHYDRO-NEU5AC
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SIALIDASE B;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: RESIDUES 30-697;
COMPND   5 SYNONYM: NEURAMINIDASE B, NANB;
COMPND   6 EC: 4.2.2.15;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE;
SOURCE   3 ORGANISM_TAXID: 170187;
SOURCE   4 STRAIN: TIGR4;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS    INTRAMOLECULAR TRANS-SIALIDASE, LYASE, GLYCOSIDASE,
KEYWDS   2 NEURAMINIDASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    H.GUT,S.J.KING,M.A.WALSH
REVDAT   3   24-FEB-09 2JKB    1       VERSN
REVDAT   2   11-NOV-08 2JKB    1       JRNL   REMARK
REVDAT   1   16-SEP-08 2JKB    0
JRNL        AUTH   H.GUT,S.J.KING,M.A.WALSH
JRNL        TITL   STRUCTURAL AND FUNCTIONAL STUDIES OF STREPTOCOCCUS
JRNL        TITL 2 PNEUMONIAE NEURAMINIDASE B: AN INTRAMOLECULAR
JRNL        TITL 3 TRANS-SIALIDASE.
JRNL        REF    FEBS LETT.                    V. 582  3348 2008
JRNL        REFN                   ISSN 0014-5793
JRNL        PMID   18775704
JRNL        DOI    10.1016/J.FEBSLET.2008.08.026
REMARK   2
REMARK   2 RESOLUTION.    1.54 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0019
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) : 1.54
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 23.93
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.1
REMARK   3   NUMBER OF REFLECTIONS             : 105364
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) : 0.163
REMARK   3   R VALUE            (WORKING SET) : 0.162
REMARK   3   FREE R VALUE                     : 0.188
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 2.500
REMARK   3   FREE R VALUE TEST SET COUNT      : 2677
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) : 1.54
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.58
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 6299
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2420
REMARK   3   BIN FREE R VALUE SET COUNT          : 157
REMARK   3   BIN FREE R VALUE                    : 0.2590
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 5439
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 44
REMARK   3   SOLVENT ATOMS            : 1024
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 12.31
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.02000
REMARK   3    B22 (A**2) : 0.03000
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): 0.073
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.073
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.047
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.258
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.968
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.957
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  5616 ; 0.010 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  3785 ; 0.001 ; 0.020
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  7631 ; 1.344 ; 1.956
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  9281 ; 0.803 ; 3.000
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   716 ; 6.919 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   262 ;35.570 ;25.153
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   977 ;11.123 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    22 ;13.412 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   826 ; 0.081 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  6417 ; 0.005 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  1134 ; 0.002 ; 0.020
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):   967 ; 0.190 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  4044 ; 0.194 ; 0.200
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2775 ; 0.176 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  3063 ; 0.082 ; 0.200
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   769 ; 0.137 ; 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):    15 ; 0.226 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):    51 ; 0.315 ; 0.200
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    71 ; 0.157 ; 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):  4467 ; 0.984 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  5599 ; 1.102 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  2591 ; 1.912 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  2032 ; 2.555 ; 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 2JKB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-AUG-08.
REMARK 100 THE PDBE ID CODE IS EBI-37278.
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        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : BM14
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.976
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL CUT
REMARK 200  OPTICS                         : TOROIDAL MIRROR
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : RAYONICS
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL2000
REMARK 200  DATA SCALING SOFTWARE          : HKL2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 108114
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.54
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.00
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.1
REMARK 200  DATA REDUNDANCY                : 3.6
REMARK 200  R MERGE                    (I) : 0.06
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 19.30
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.60
REMARK 200  COMPLETENESS FOR SHELL     (%) : 81.6
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.0
REMARK 200  R MERGE FOR SHELL          (I) : 0.35
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 2.60
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: HOMOLOGY MODEL
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 49.7
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 6000, 200 MM TRIS PH
REMARK 280  8.0
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       38.35950
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       59.03950
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       41.37300
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       59.03950
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       38.35950
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       41.37300
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    12
REMARK 465     HIS A    13
REMARK 465     HIS A    14
REMARK 465     HIS A    15
REMARK 465     HIS A    16
REMARK 465     HIS A    17
REMARK 465     HIS A    18
REMARK 465     SER A    19
REMARK 465     SER A    20
REMARK 465     GLY A    21
REMARK 465     LEU A    22
REMARK 465     GLU A    23
REMARK 465     VAL A    24
REMARK 465     LEU A    25
REMARK 465     PHE A    26
REMARK 465     GLN A    27
REMARK 465     GLY A    28
REMARK 465     PRO A    29
REMARK 465     ASN A    30
REMARK 465     GLU A    31
REMARK 465     LEU A    32
REMARK 465     ASN A    33
REMARK 465     TYR A    34
REMARK 465     GLY A    35
REMARK 465     GLN A    36
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  2222  -  O    HOH A  2940              2.09
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    ASP A 262   CB  -  CG  -  OD1 ANGL. DEV. =   5.7 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500 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  51       63.99   -113.65
REMARK 500    ALA A  78       89.52   -153.57
REMARK 500    LYS A  80       57.08   -142.25
REMARK 500    GLN A 240       18.22     59.68
REMARK 500    ILE A 246       61.84     67.06
REMARK 500    SER A 273     -171.45   -171.82
REMARK 500    ASP A 327       88.71     68.56
REMARK 500    PRO A 534       40.89    -86.16
REMARK 500    TYR A 651      119.56   -160.45
REMARK 500    ALA A 652     -120.42   -125.99
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 ILE A  365     ASN A  366                  -39.37
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 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 SKD A1698
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1699
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1700
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1704
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2VW0   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM
REMARK 900   STREPTOCOCCUS PNEUMONIAE
REMARK 900 RELATED ID: 2VW1   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM
REMARK 900   STREPTOCOCCUS PNEUMONIAE
REMARK 900 RELATED ID: 2VW2   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM
REMARK 900   STREPTOCOCCUS PNEUMONIAE
DBREF  2JKB A   12    29  PDB    2JKB     2JKB            12     29
DBREF  2JKB A   30   697  UNP    Q54727   NANB_STRPN      30    697
SEQRES   1 A  686  ALA HIS HIS HIS HIS HIS HIS SER SER GLY LEU GLU VAL
SEQRES   2 A  686  LEU PHE GLN GLY PRO ASN GLU LEU ASN TYR GLY GLN LEU
SEQRES   3 A  686  SER ILE SER PRO ILE PHE GLN GLY GLY SER TYR GLN LEU
SEQRES   4 A  686  ASN ASN LYS SER ILE ASP ILE SER SER LEU LEU LEU ASP
SEQRES   5 A  686  LYS LEU SER GLY GLU SER GLN THR VAL VAL MET LYS PHE
SEQRES   6 A  686  LYS ALA ASP LYS PRO ASN SER LEU GLN ALA LEU PHE GLY
SEQRES   7 A  686  LEU SER ASN SER LYS ALA GLY PHE LYS ASN ASN TYR PHE
SEQRES   8 A  686  SER ILE PHE MET ARG ASP SER GLY GLU ILE GLY VAL GLU
SEQRES   9 A  686  ILE ARG ASP ALA GLN LYS GLY ILE ASN TYR LEU PHE SER
SEQRES  10 A  686  ARG PRO ALA SER LEU TRP GLY LYS HIS LYS GLY GLN ALA
SEQRES  11 A  686  VAL GLU ASN THR LEU VAL PHE VAL SER ASP SER LYS ASP
SEQRES  12 A  686  LYS THR TYR THR MET TYR VAL ASN GLY ILE GLU VAL PHE
SEQRES  13 A  686  SER GLU THR VAL ASP THR PHE LEU PRO ILE SER ASN ILE
SEQRES  14 A  686  ASN GLY ILE ASP LYS ALA THR LEU GLY ALA VAL ASN ARG
SEQRES  15 A  686  GLU GLY LYS GLU HIS TYR LEU ALA LYS GLY SER ILE ASP
SEQRES  16 A  686  GLU ILE SER LEU PHE ASN LYS ALA ILE SER ASP GLN GLU
SEQRES  17 A  686  VAL SER THR ILE PRO LEU SER ASN PRO PHE GLN LEU ILE
SEQRES  18 A  686  PHE GLN SER GLY ASP SER THR GLN ALA ASN TYR PHE ARG
SEQRES  19 A  686  ILE PRO THR LEU TYR THR LEU SER SER GLY ARG VAL LEU
SEQRES  20 A  686  SER SER ILE ASP ALA ARG TYR GLY GLY THR HIS ASP SER
SEQRES  21 A  686  LYS SER LYS ILE ASN ILE ALA THR SER TYR SER ASP ASP
SEQRES  22 A  686  ASN GLY LYS THR TRP SER GLU PRO ILE PHE ALA MET LYS
SEQRES  23 A  686  PHE ASN ASP TYR GLU GLU GLN LEU VAL TYR TRP PRO ARG
SEQRES  24 A  686  ASP ASN LYS LEU LYS ASN SER GLN ILE SER GLY SER ALA
SEQRES  25 A  686  SER PHE ILE ASP SER SER ILE VAL GLU ASP LYS LYS SER
SEQRES  26 A  686  GLY LYS THR ILE LEU LEU ALA ASP VAL MET PRO ALA GLY
SEQRES  27 A  686  ILE GLY ASN ASN ASN ALA ASN LYS ALA ASP SER GLY PHE
SEQRES  28 A  686  LYS GLU ILE ASN GLY HIS TYR TYR LEU LYS LEU LYS LYS
SEQRES  29 A  686  ASN GLY ASP ASN ASP PHE ARG TYR THR VAL ARG GLU ASN
SEQRES  30 A  686  GLY VAL VAL TYR ASN GLU THR THR ASN LYS PRO THR ASN
SEQRES  31 A  686  TYR THR ILE ASN ASP LYS TYR GLU VAL LEU GLU GLY GLY
SEQRES  32 A  686  LYS SER LEU THR VAL GLU GLN TYR SER VAL ASP PHE ASP
SEQRES  33 A  686  SER GLY SER LEU ARG GLU ARG HIS ASN GLY LYS GLN VAL
SEQRES  34 A  686  PRO MET ASN VAL PHE TYR LYS ASP SER LEU PHE LYS VAL
SEQRES  35 A  686  THR PRO THR ASN TYR ILE ALA MET THR THR SER GLN ASN
SEQRES  36 A  686  ARG GLY GLU SER TRP GLU GLN PHE LYS LEU LEU PRO PRO
SEQRES  37 A  686  PHE LEU GLY GLU LYS HIS ASN GLY THR TYR LEU CYS PRO
SEQRES  38 A  686  GLY GLN GLY LEU ALA LEU LYS SER SER ASN ARG LEU ILE
SEQRES  39 A  686  PHE ALA THR TYR THR SER GLY GLU LEU THR TYR LEU ILE
SEQRES  40 A  686  SER ASP ASP SER GLY GLN THR TRP LYS LYS SER SER ALA
SEQRES  41 A  686  SER ILE PRO PHE LYS ASN ALA THR ALA GLU ALA GLN MET
SEQRES  42 A  686  VAL GLU LEU ARG ASP GLY VAL ILE ARG THR PHE PHE ARG
SEQRES  43 A  686  THR THR THR GLY LYS ILE ALA TYR MET THR SER ARG ASP
SEQRES  44 A  686  SER GLY GLU THR TRP SER LYS VAL SER TYR ILE ASP GLY
SEQRES  45 A  686  ILE GLN GLN THR SER TYR GLY THR GLN VAL SER ALA ILE
SEQRES  46 A  686  LYS TYR SER GLN LEU ILE ASP GLY LYS GLU ALA VAL ILE
SEQRES  47 A  686  LEU SER THR PRO ASN SER ARG SER GLY ARG LYS GLY GLY
SEQRES  48 A  686  GLN LEU VAL VAL GLY LEU VAL ASN LYS GLU ASP ASP SER
SEQRES  49 A  686  ILE ASP TRP LYS TYR HIS TYR ASP ILE ASP LEU PRO SER
SEQRES  50 A  686  TYR GLY TYR ALA TYR SER ALA ILE THR GLU LEU PRO ASN
SEQRES  51 A  686  HIS HIS ILE GLY VAL LEU PHE GLU LYS TYR ASP SER TRP
SEQRES  52 A  686  SER ARG ASN GLU LEU HIS LEU SER ASN VAL VAL GLN TYR
SEQRES  53 A  686  ILE ASP LEU GLU ILE ASN ASP LEU THR LYS
HET    SKD  A1698      20
HET    EDO  A1699       4
HET    EDO  A1700       4
HET    EDO  A1701       4
HET    EDO  A1702       4
HET    EDO  A1703       4
HET    EDO  A1704       4
HETNAM     EDO 1,2-ETHANEDIOL
HETNAM     SKD 2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-
HETNAM   2 SKD  HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-
HETNAM   3 SKD  CARBOXYLIC ACID
FORMUL   2  EDO    6(C2 H6 O2)
FORMUL   3  SKD    C11 H17 N O8
FORMUL   4  HOH   *1024(H2 O1)
HELIX    1   1 ILE A   57  LEU A   62  1                                   6
HELIX    2   2 ASP A   63  LEU A   65  5                                   3
HELIX    3   3 PRO A  176  ILE A  180  5                                   5
HELIX    4   4 SER A  216  THR A  222  1                                   7
HELIX    5   5 GLU A  691  THR A  696  1                                   6
SHEET    1  AA 6 PHE A  43  ASN A  51  0
SHEET    2  AA 6 LYS A 202  PHE A 211 -1  O  GLY A 203   N  LEU A  50
SHEET    3  AA 6 GLN A  70  LYS A  77 -1  O  THR A  71   N  PHE A 211
SHEET    4  AA 6 ASN A 144  ASP A 151 -1  O  ASN A 144   N  PHE A  76
SHEET    5  AA 6 THR A 156  VAL A 161 -1  O  THR A 156   N  ASP A 151
SHEET    6  AA 6 ILE A 164  THR A 170 -1  O  ILE A 164   N  VAL A 161
SHEET    1  AB 6 ILE A  55  ASP A  56  0
SHEET    2  AB 6 LYS A 185  LEU A 188 -1  O  LEU A 188   N  ILE A  55
SHEET    3  AB 6 LEU A  84  SER A  91 -1  O  GLY A  89   N  THR A 187
SHEET    4  AB 6 TYR A 101  ARG A 107 -1  O  PHE A 102   N  LEU A  90
SHEET    5  AB 6 ILE A 112  ASP A 118 -1  O  GLY A 113   N  PHE A 105
SHEET    6  AB 6 ILE A 123  ARG A 129 -1  O  ILE A 123   N  ASP A 118
SHEET    1  AC 2 LYS A 136  HIS A 137  0
SHEET    2  AC 2 GLN A 140  ALA A 141 -1  O  GLN A 140   N  HIS A 137
SHEET    1  AD 2 VAL A 191  ARG A 193  0
SHEET    2  AD 2 LYS A 196  HIS A 198 -1  O  LYS A 196   N  ARG A 193
SHEET    1  AE 3 TYR A 243  ARG A 245  0
SHEET    2  AE 3 VAL A 257  ARG A 264 -1  O  ASP A 262   N  ARG A 245
SHEET    3  AE 3 TYR A 250  THR A 251 -1  O  TYR A 250   N  LEU A 258
SHEET    1  AF 4 TYR A 243  ARG A 245  0
SHEET    2  AF 4 VAL A 257  ARG A 264 -1  O  ASP A 262   N  ARG A 245
SHEET    3  AF 4 ILE A 275  SER A 282 -1  O  ASN A 276   N  ALA A 263
SHEET    4  AF 4 ILE A 293  MET A 296 -1  O  ILE A 293   N  THR A 279
SHEET    1  AG 5 LYS A 475  LEU A 476  0
SHEET    2  AG 5 TYR A 458  SER A 464 -1  O  MET A 461   N  LYS A 475
SHEET    3  AG 5 THR A 339  MET A 346 -1  O  THR A 339   N  SER A 464
SHEET    4  AG 5 SER A 324  GLU A 332 -1  O  SER A 324   N  MET A 346
SHEET    5  AG 5 GLY A 493  GLN A 494  1  O  GLY A 493   N  ILE A 330
SHEET    1  AH 7 PHE A 362  GLU A 364  0
SHEET    2  AH 7 TYR A 369  LYS A 375 -1  O  TYR A 370   N  LYS A 363
SHEET    3  AH 7 TYR A 383  VAL A 385 -1  O  TYR A 383   N  LEU A 373
SHEET    4  AH 7 VAL A 390  ASN A 393 -1  O  TYR A 392   N  THR A 384
SHEET    5  AH 7 LYS A 398  ILE A 404 -1  O  LYS A 398   N  ASN A 393
SHEET    6  AH 7 VAL A 410  GLU A 412 -1  O  LEU A 411   N  THR A 403
SHEET    7  AH 7 LYS A 415  SER A 416 -1  O  LYS A 415   N  GLU A 412
SHEET    1  AI 3 PHE A 362  GLU A 364  0
SHEET    2  AI 3 TYR A 369  LYS A 375 -1  O  TYR A 370   N  LYS A 363
SHEET    3  AI 3 PHE A 451  LYS A 452 -1  O  LYS A 452   N  LYS A 374
SHEET    1  AJ 2 THR A 418  ASP A 425  0
SHEET    2  AJ 2 ARG A 432  PRO A 441 -1  O  ARG A 432   N  ASP A 425
SHEET    1  AK 3 TYR A 489  LEU A 490  0
SHEET    2  AK 3 LEU A 504  THR A 510 -1  O  TYR A 509   N  TYR A 489
SHEET    3  AK 3 LEU A 496  ALA A 497 -1  O  LEU A 496   N  ILE A 505
SHEET    1  AL 4 TYR A 489  LEU A 490  0
SHEET    2  AL 4 LEU A 504  THR A 510 -1  O  TYR A 509   N  TYR A 489
SHEET    3  AL 4 GLU A 513  SER A 519 -1  O  GLU A 513   N  THR A 510
SHEET    4  AL 4 LYS A 527  SER A 532 -1  O  LYS A 527   N  ILE A 518
SHEET    1  AM 4 ALA A 542  ARG A 548  0
SHEET    2  AM 4 VAL A 551  PHE A 556 -1  O  VAL A 551   N  LEU A 547
SHEET    3  AM 4 ALA A 564  SER A 568 -1  O  ALA A 564   N  PHE A 556
SHEET    4  AM 4 SER A 579  TYR A 580 -1  O  SER A 579   N  TYR A 565
SHEET    1  AN 4 SER A 594  ILE A 602  0
SHEET    2  AN 4 LYS A 605  PRO A 613 -1  O  LYS A 605   N  ILE A 602
SHEET    3  AN 4 GLY A 622  VAL A 629 -1  O  GLN A 623   N  THR A 612
SHEET    4  AN 4 ILE A 636  ASP A 643 -1  O  ASP A 637   N  LEU A 628
SHEET    1  AO 3 SER A 654  GLU A 658  0
SHEET    2  AO 3 ILE A 664  GLU A 669 -1  O  GLY A 665   N  THR A 657
SHEET    3  AO 3 VAL A 685  LEU A 690 -1  O  GLN A 686   N  PHE A 668
CISPEP   1 SER A  271    LYS A  272          0         2.64
SITE     1 AC1 17 ARG A 245  ILE A 246  ARG A 264  ASP A 270
SITE     2 AC1 17 ILE A 326  ASP A 327  ASP A 344  ASN A 352
SITE     3 AC1 17 THR A 539  GLU A 541  ARG A 557  ARG A 619
SITE     4 AC1 17 TYR A 653  TRP A 674  HOH A2457  HOH A3012
SITE     5 AC1 17 HOH A3013
SITE     1 AC2  7 LEU A  84  SER A 103  GLU A 115  TYR A 199
SITE     2 AC2  7 LYS A 335  HOH A3014  HOH A3015
SITE     1 AC3  6 TYR A 458  ILE A 459  LEU A 477  PRO A 478
SITE     2 AC3  6 PHE A 480  HOH A3016
SITE     1 AC4 10 VAL A 385  ILE A 404  ASN A 405  ASP A 406
SITE     2 AC4 10 TYR A 408  LYS A 475  HOH A2629  HOH A3017
SITE     3 AC4 10 HOH A3018  HOH A3019
SITE     1 AC5  6 THR A 251  GLN A 494  ILE A 596  THR A 657
SITE     2 AC5  6 HOH A2956  HOH A3020
SITE     1 AC6  6 SER A 617  LYS A 620  SER A 648  HOH A2911
SITE     2 AC6  6 HOH A3021  HOH A3022
SITE     1 AC7  8 ARG A 256  ASN A 466  ARG A 467  GLU A 469
SITE     2 AC7  8 SER A 617  HOH A2444  HOH A3023  HOH A3024
CRYST1   76.719   82.746  118.079  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      0.013035  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012085  0.000000        0.00000
SCALE3      0.000000  0.000000  0.008469        0.00000
      
PROCHECK
Go to PROCHECK summary
 References