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PDBsum entry 2ber

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Hydrolase PDB id
2ber
Jmol
Contents
Protein chain
601 a.a.
Ligands
SLB
Metals
_NA
Waters ×837
HEADER    HYDROLASE                               30-NOV-04   2BER
TITLE     Y370G ACTIVE SITE MUTANT OF THE SIALIDASE FROM
TITLE    2 MICROMONOSPORA VIRIDIFACIENS IN COMPLEX WITH BETA-NEU5AC
TITLE    3 (SIALIC ACID).
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: BACTERIAL SIALIDASE;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: RESIDUES 47-647;
COMPND   5 SYNONYM: NEURAMINIDASE;
COMPND   6 EC: 3.2.1.18;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: MICROMONOSPORA VIRIDIFACIENS;
SOURCE   3 ORGANISM_TAXID: 1881;
SOURCE   4 ATCC: 31146;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET28A
KEYWDS    GLYCOSIDASE, HYDROLASE, SIALIDASE, BETA-PROPELLER,
KEYWDS   2 MICROMONOSPORA VIRIDIFACIENS
EXPDTA    X-RAY DIFFRACTION
AUTHOR    S.NEWSTEAD,J.N.WATSON,A.J.BENNET,G.L.TAYLOR
REVDAT   4   24-FEB-09 2BER    1       VERSN
REVDAT   3   29-JUN-05 2BER    1       JRNL
REVDAT   2   02-JUN-05 2BER    1       JRNL
REVDAT   1   04-APR-05 2BER    0
JRNL        AUTH   S.NEWSTEAD,J.N.WATSON,T.L.KNOLL,A.J.BENNET,
JRNL        AUTH 2 G.L.TAYLOR
JRNL        TITL   STRUCTURE AND MECHANISM OF ACTION OF AN INVERTING
JRNL        TITL 2 MUTANT SIALIDASE.
JRNL        REF    BIOCHEMISTRY                  V.  44  9117 2005
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   15966735
JRNL        DOI    10.1021/BI050517T
REMARK   2
REMARK   2 RESOLUTION.    1.8  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) : 1.80
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 105.41
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 87.0
REMARK   3   NUMBER OF REFLECTIONS             : 43865
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) : 0.143
REMARK   3   R VALUE            (WORKING SET) : 0.140
REMARK   3   FREE R VALUE                     : 0.199
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 2348
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) : 1.80
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.85
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 3118
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : 0.1720
REMARK   3   BIN FREE R VALUE SET COUNT          : 180
REMARK   3   BIN FREE R VALUE                    : 0.2480
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 4545
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 22
REMARK   3   SOLVENT ATOMS            : 837
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 13.61
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 0.84000
REMARK   3    B22 (A**2) : 0.59000
REMARK   3    B33 (A**2) : -1.15000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.70000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.133
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.134
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.079
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.499
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.967
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.936
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  4676 ; 0.020 ; 0.021
REMARK   3   BOND LENGTHS OTHERS               (A):  4130 ; 0.001 ; 0.020
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  6392 ; 1.779 ; 1.951
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  9570 ; 0.933 ; 3.000
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   600 ; 7.166 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   212 ;32.926 ;23.302
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   681 ;11.976 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    43 ;16.689 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   709 ; 0.113 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  5354 ; 0.009 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):   962 ; 0.001 ; 0.020
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):   790 ; 0.215 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  4261 ; 0.202 ; 0.200
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2245 ; 0.172 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  2835 ; 0.086 ; 0.200
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   502 ; 0.189 ; 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):    13 ; 0.213 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):    52 ; 0.267 ; 0.200
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    52 ; 0.188 ; 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):  2988 ; 1.020 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  4820 ; 1.621 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1754 ; 2.562 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1572 ; 3.817 ; 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 : BABINET MODEL WITH 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 2BER COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-04.
REMARK 100 THE PDBE ID CODE IS EBI-21804.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 23-APR-04
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 5.00
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID14-3
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.931
REMARK 200  MONOCHROMATOR                  : DIAMOND (111), GE(220)
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 53080
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.790
REMARK 200  RESOLUTION RANGE LOW       (A) : 34.940
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 6.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 87.3
REMARK 200  DATA REDUNDANCY                : 2.700
REMARK 200  R MERGE                    (I) : 0.09000
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 11.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.90
REMARK 200  COMPLETENESS FOR SHELL     (%) : 87.3
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.30
REMARK 200  R MERGE FOR SHELL          (I) : 0.22000
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 3.100
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 1W8O
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 41.4
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.1
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16 % PEG 3350, 0.2 M SODIUM
REMARK 280  FLUORIDE.
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       24.76750
REMARK 290   SMTRY3   2  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 400
REMARK 400 COMPOUND
REMARK 400  ENGINEERED RESIDUE TYR 370 GLY, CHAIN A
REMARK 400  RELEASES SIALIC ACIDS FOR USE AS SOURCE OF CARBON AND ENERGY
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   420  -  O    HOH A  2566              2.00
REMARK 500   OE2  GLU A   584  -  O    HOH A  2752              2.18
REMARK 500   CA   LEU A   589  -  O    HOH A  2756              2.03
REMARK 500   O    LEU A   589  -  O    HOH A  2756              2.00
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  92   CB  -  CG  -  OD1 ANGL. DEV. =   5.6 DEGREES
REMARK 500    ASP A 166   CB  -  CG  -  OD2 ANGL. DEV. =  -5.6 DEGREES
REMARK 500    ASP A 412   CB  -  CG  -  OD1 ANGL. DEV. =   6.0 DEGREES
REMARK 500    MET A 458   CG  -  SD  -  CE  ANGL. DEV. =  10.5 DEGREES
REMARK 500    ARG A 508   NE  -  CZ  -  NH1 ANGL. DEV. =   4.3 DEGREES
REMARK 500    ARG A 508   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.9 DEGREES
REMARK 500    ARG A 553   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES
REMARK 500    ARG A 553   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.3 DEGREES
REMARK 500    ARG A 602   NE  -  CZ  -  NH1 ANGL. DEV. =   7.2 DEGREES
REMARK 500    ARG A 602   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.8 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    ILE A  69       76.43     83.31
REMARK 500    THR A 123     -129.21   -111.81
REMARK 500    ASP A 131       72.50     71.66
REMARK 500    GLN A 151      -87.73   -126.83
REMARK 500    ASP A 259     -155.05   -170.95
REMARK 500    THR A 309       79.47     82.45
REMARK 500    MET A 368       92.60   -161.78
REMARK 500    ALA A 581      -97.19   -117.33
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                              NA A1649  NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 639   O
REMARK 620 2 ASN A 533   O   101.9
REMARK 620 3 ASN A 528   O    87.5 165.8
REMARK 620 4 ASP A 531   OD1 137.4  90.9  75.1
REMARK 620 5 THR A 536   OG1 143.1  88.2  90.5  76.7
REMARK 620 N                    1     2     3     4
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 SLB A1648
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  NA A1649
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1EUR   RELATED DB: PDB
REMARK 900  SIALIDASE
REMARK 900 RELATED ID: 1EUS   RELATED DB: PDB
REMARK 900  SIALIDASE COMPLEXED WITH 2-DEOXY-2,3-
REMARK 900  DEHYDRO-N- ACETYLNEURAMINIC ACID
REMARK 900 RELATED ID: 1EUT   RELATED DB: PDB
REMARK 900  SIALIDASE, LARGE 68KD FORM, COMPLEXED WITH
REMARK 900  GALACTOSE
REMARK 900 RELATED ID: 1EUU   RELATED DB: PDB
REMARK 900  SIALIDASE OR NEURAMINIDASE, LARGE 68KD FORM
REMARK 900 RELATED ID: 1W8N   RELATED DB: PDB
REMARK 900  CONTRIBUTION OF THE ACTIVE SITE ASPARTIC
REMARK 900  ACID TO CATALYSIS IN THE BACTERIAL
REMARK 900  NEURAMINIDASE FROM MICROMONOSPORA VIRIDIFACIENS.
REMARK 900 RELATED ID: 1W8O   RELATED DB: PDB
REMARK 900  CONTRIBUTION OF THE ACTIVE SITE ASPARTIC
REMARK 900  ACID TO CATALYSIS IN THE BACTERIAL
REMARK 900  NEURAMINIDASE FROM MICROMONOSPORA VIRIDIFACIENS
REMARK 900 RELATED ID: 1WCQ   RELATED DB: PDB
REMARK 900  MUTAGENESIS OF THE NUCLEOPHILIC TYROSINE IN
REMARK 900  A BACTERIAL SIALIDASE TO PHENYLALANINE.
DBREF  2BER A   47   647  UNP    Q02834   NANH_MICVI      47    647
SEQADV 2BER GLY A  370  UNP  Q02834    TYR   370 ENGINEERED MUTATION
SEQRES   1 A  601  GLY GLU PRO LEU TYR THR GLU GLN ASP LEU ALA VAL ASN
SEQRES   2 A  601  GLY ARG GLU GLY PHE PRO ASN TYR ARG ILE PRO ALA LEU
SEQRES   3 A  601  THR VAL THR PRO ASP GLY ASP LEU LEU ALA SER TYR ASP
SEQRES   4 A  601  GLY ARG PRO THR GLY ILE ASP ALA PRO GLY PRO ASN SER
SEQRES   5 A  601  ILE LEU GLN ARG ARG SER THR ASP GLY GLY ARG THR TRP
SEQRES   6 A  601  GLY GLU GLN GLN VAL VAL SER ALA GLY GLN THR THR ALA
SEQRES   7 A  601  PRO ILE LYS GLY PHE SER ASP PRO SER TYR LEU VAL ASP
SEQRES   8 A  601  ARG GLU THR GLY THR ILE PHE ASN PHE HIS VAL TYR SER
SEQRES   9 A  601  GLN ARG GLN GLY PHE ALA GLY SER ARG PRO GLY THR ASP
SEQRES  10 A  601  PRO ALA ASP PRO ASN VAL LEU HIS ALA ASN VAL ALA THR
SEQRES  11 A  601  SER THR ASP GLY GLY LEU THR TRP SER HIS ARG THR ILE
SEQRES  12 A  601  THR ALA ASP ILE THR PRO ASP PRO GLY TRP ARG SER ARG
SEQRES  13 A  601  PHE ALA ALA SER GLY GLU GLY ILE GLN LEU ARG TYR GLY
SEQRES  14 A  601  PRO HIS ALA GLY ARG LEU ILE GLN GLN TYR THR ILE ILE
SEQRES  15 A  601  ASN ALA ALA GLY ALA PHE GLN ALA VAL SER VAL TYR SER
SEQRES  16 A  601  ASP ASP HIS GLY ARG THR TRP ARG ALA GLY GLU ALA VAL
SEQRES  17 A  601  GLY VAL GLY MET ASP GLU ASN LYS THR VAL GLU LEU SER
SEQRES  18 A  601  ASP GLY ARG VAL LEU LEU ASN SER ARG ASP SER ALA ARG
SEQRES  19 A  601  SER GLY TYR ARG LYS VAL ALA VAL SER THR ASP GLY GLY
SEQRES  20 A  601  HIS SER TYR GLY PRO VAL THR ILE ASP ARG ASP LEU PRO
SEQRES  21 A  601  ASP PRO THR ASN ASN ALA SER ILE ILE ARG ALA PHE PRO
SEQRES  22 A  601  ASP ALA PRO ALA GLY SER ALA ARG ALA LYS VAL LEU LEU
SEQRES  23 A  601  PHE SER ASN ALA ALA SER GLN THR SER ARG SER GLN GLY
SEQRES  24 A  601  THR ILE ARG MET SER CYS ASP ASP GLY GLN THR TRP PRO
SEQRES  25 A  601  VAL SER LYS VAL PHE GLN PRO GLY SER MET SER GLY SER
SEQRES  26 A  601  THR LEU THR ALA LEU PRO ASP GLY THR TYR GLY LEU LEU
SEQRES  27 A  601  TYR GLU PRO GLY THR GLY ILE ARG TYR ALA ASN PHE ASN
SEQRES  28 A  601  LEU ALA TRP LEU GLY GLY ILE CYS ALA PRO PHE THR ILE
SEQRES  29 A  601  PRO ASP VAL ALA LEU GLU PRO GLY GLN GLN VAL THR VAL
SEQRES  30 A  601  PRO VAL ALA VAL THR ASN GLN SER GLY ILE ALA VAL PRO
SEQRES  31 A  601  LYS PRO SER LEU GLN LEU ASP ALA SER PRO ASP TRP GLN
SEQRES  32 A  601  VAL GLN GLY SER VAL GLU PRO LEU MET PRO GLY ARG GLN
SEQRES  33 A  601  ALA LYS GLY GLN VAL THR ILE THR VAL PRO ALA GLY THR
SEQRES  34 A  601  THR PRO GLY ARG TYR ARG VAL GLY ALA THR LEU ARG THR
SEQRES  35 A  601  SER ALA GLY ASN ALA SER THR THR PHE THR VAL THR VAL
SEQRES  36 A  601  GLY LEU LEU ASP GLN ALA ARG MET SER ILE ALA ASP VAL
SEQRES  37 A  601  ASP SER GLU GLU THR ALA ARG GLU ASP GLY ARG ALA SER
SEQRES  38 A  601  ASN VAL ILE ASP GLY ASN PRO SER THR PHE TRP HIS THR
SEQRES  39 A  601  GLU TRP SER ARG ALA ASP ALA PRO GLY TYR PRO HIS ARG
SEQRES  40 A  601  ILE SER LEU ASP LEU GLY GLY THR HIS THR ILE SER GLY
SEQRES  41 A  601  LEU GLN TYR THR ARG ARG GLN ASN SER ALA ASN GLU GLN
SEQRES  42 A  601  VAL ALA ASP TYR GLU ILE TYR THR SER LEU ASN GLY THR
SEQRES  43 A  601  THR TRP ASP GLY PRO VAL ALA SER GLY ARG PHE THR THR
SEQRES  44 A  601  SER LEU ALA PRO GLN ARG ALA VAL PHE PRO ALA ARG ASP
SEQRES  45 A  601  ALA ARG TYR ILE ARG LEU VAL ALA LEU SER GLU GLN THR
SEQRES  46 A  601  GLY HIS LYS TYR ALA ALA VAL ALA GLU LEU GLU VAL GLU
SEQRES  47 A  601  GLY GLN ARG
HET    SLB  A1648      21
HET     NA  A1649       1
HETNAM     SLB 5-N-ACETYL-BETA-D-NEURAMINIC ACID
HETNAM      NA SODIUM ION
FORMUL   2  SLB    C11 H19 N O9
FORMUL   3   NA    NA 1+
FORMUL   4  HOH   *837(H2 O1)
HELIX    1   1 THR A  190  THR A  194  5                                   5
HELIX    2   2 ALA A  326  LYS A  329  5                                   4
HELIX    3   3 ASN A  397  GLY A  402  1                                   6
HELIX    4   4 ASP A  505  MET A  509  5                                   5
HELIX    5   5 ARG A  525  ASP A  531  5                                   7
SHEET    1  AA 4 TYR A  51  VAL A  58  0
SHEET    2  AA 4 GLY A 390  PHE A 396 -1  O  ILE A 391   N  LEU A  56
SHEET    3  AA 4 TYR A 381  TYR A 385 -1  O  TYR A 381   N  PHE A 396
SHEET    4  AA 4 SER A 371  ALA A 375 -1  O  THR A 372   N  LEU A 384
SHEET    1  AB 4 TYR A  67  VAL A  74  0
SHEET    2  AB 4 LEU A  80  GLY A  86 -1  O  LEU A  81   N  THR A  73
SHEET    3  AB 4 SER A  98  SER A 104 -1  O  SER A  98   N  GLY A  86
SHEET    4  AB 4 GLN A 115  SER A 118 -1  O  GLN A 115   N  GLN A 101
SHEET    1  AC 5 SER A 185  THR A 188  0
SHEET    2  AC 5 HIS A 171  SER A 177 -1  O  VAL A 174   N  ARG A 187
SHEET    3  AC 5 ILE A 143  SER A 150 -1  O  ILE A 143   N  SER A 177
SHEET    4  AC 5 GLY A 128  VAL A 136 -1  O  GLY A 128   N  SER A 150
SHEET    5  AC 5 GLY A 207  GLU A 208  1  O  GLY A 207   N  TYR A 134
SHEET    1  AD 3 SER A 201  ALA A 204  0
SHEET    2  AD 3 LEU A 221  ILE A 228 -1  O  THR A 226   N  PHE A 203
SHEET    3  AD 3 ILE A 210  GLN A 211 -1  O  ILE A 210   N  ILE A 222
SHEET    1  AE 4 SER A 201  ALA A 204  0
SHEET    2  AE 4 LEU A 221  ILE A 228 -1  O  THR A 226   N  PHE A 203
SHEET    3  AE 4 PHE A 234  SER A 241 -1  O  GLN A 235   N  ILE A 227
SHEET    4  AE 4 ARG A 249  ALA A 250 -1  O  ARG A 249   N  TYR A 240
SHEET    1  AF 4 ASN A 261  GLU A 265  0
SHEET    2  AF 4 VAL A 271  SER A 275 -1  O  LEU A 272   N  VAL A 264
SHEET    3  AF 4 TYR A 283  SER A 289 -1  O  LYS A 285   N  SER A 275
SHEET    4  AF 4 THR A 300  PRO A 306 -1  O  THR A 300   N  VAL A 286
SHEET    1  AG 4 SER A 313  ARG A 316  0
SHEET    2  AG 4 LEU A 331  ALA A 336 -1  O  LEU A 332   N  ILE A 315
SHEET    3  AG 4 SER A 343  SER A 350 -1  O  THR A 346   N  ASN A 335
SHEET    4  AG 4 VAL A 359  SER A 367 -1  O  VAL A 359   N  MET A 349
SHEET    1  AH 4 PHE A 408  THR A 409  0
SHEET    2  AH 4 GLN A 419  THR A 428 -1  O  ALA A 426   N  THR A 409
SHEET    3  AH 4 GLN A 462  VAL A 471 -1  O  ALA A 463   N  VAL A 427
SHEET    4  AH 4 GLN A 449  VAL A 454 -1  O  GLN A 449   N  THR A 470
SHEET    1  AI 4 VAL A 413  LEU A 415  0
SHEET    2  AI 4 GLY A 491  VAL A 501  1  O  THR A 498   N  VAL A 413
SHEET    3  AI 4 GLY A 478  THR A 488 -1  O  GLY A 478   N  VAL A 501
SHEET    4  AI 4 SER A 439  ASP A 443 -1  O  SER A 439   N  ARG A 487
SHEET    1  AJ 5 SER A 510  VAL A 514  0
SHEET    2  AJ 5 HIS A 552  ARG A 571 -1  O  SER A 555   N  ALA A 512
SHEET    3  AJ 5 GLN A 610  ALA A 626 -1  O  GLN A 610   N  TYR A 569
SHEET    4  AJ 5 ASP A 582  SER A 588 -1  O  GLU A 584   N  VAL A 625
SHEET    5  AJ 5 ASP A 595  ARG A 602 -1  O  ASP A 595   N  THR A 587
SHEET    1  AK 4 SER A 510  VAL A 514  0
SHEET    2  AK 4 HIS A 552  ARG A 571 -1  O  SER A 555   N  ALA A 512
SHEET    3  AK 4 ALA A 637  GLY A 645 -1  N  ALA A 639   O  THR A 570
SHEET    4  AK 4 TRP A 538  HIS A 539 -1  O  TRP A 538   N  VAL A 638
SSBOND   1 CYS A  351    CYS A  405                          1555   1555  2.04
LINK        NA    NA A1649                 O   ALA A 639     1555   1555  2.38
LINK        NA    NA A1649                 O   ASN A 533     1555   1555  2.30
LINK        NA    NA A1649                 O   ASN A 528     1555   1555  2.30
LINK        NA    NA A1649                 OD1 ASP A 531     1555   1555  2.44
LINK        NA    NA A1649                 OG1 THR A 536     1555   1555  2.60
CISPEP   1 ALA A   93    PRO A   94          0         6.85
CISPEP   2 ALA A  124    PRO A  125          0        -9.10
CISPEP   3 TYR A  550    PRO A  551          0         3.19
CISPEP   4 GLY A  596    PRO A  597          0        -3.77
SITE     1 AC1 15 ARG A  68  ILE A  69  ARG A  87  ASP A  92
SITE     2 AC1 15 ASP A 131  PHE A 203  ASP A 259  GLU A 260
SITE     3 AC1 15 ARG A 276  ARG A 342  HOH A2088  HOH A2458
SITE     4 AC1 15 HOH A2834  HOH A2836  HOH A2837
SITE     1 AC2  5 ASN A 528  ASP A 531  ASN A 533  THR A 536
SITE     2 AC2  5 ALA A 639
CRYST1   55.440   49.535  107.041  90.00 101.74  90.00 P 1 21 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      0.018038  0.000000  0.003750        0.00000
SCALE2      0.000000  0.020188  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009542        0.00000
      
PROCHECK
Go to PROCHECK summary
 References