HEADER HYDROLASE 17-DEC-07 2VK5
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 4 16-FEB-11 2VK5 1 VERSN
REVDAT 3 24-FEB-09 2VK5 1 VERSN
REVDAT 2 08-APR-08 2VK5 1 JRNL REMARK
REVDAT 1 22-JAN-08 2VK5 0
JRNL AUTH S.L.NEWSTEAD,J.A.POTTER,J.C.WILSON,G.XU,C.H.CHIEN,A.G.WATTS,
JRNL AUTH 2 S.G.WITHERS,G.L.TAYLOR
JRNL TITL THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND
JRNL TITL 2 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. 0.97 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELX
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0
REMARK 3 COMPLETENESS FOR RANGE (%) : 98
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 281317
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3584
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 14
REMARK 3 SOLVENT ATOMS : 1030
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL
REMARK 3 NUMBER OF RESTRAINTS : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.017
REMARK 3 ANGLE DISTANCES (A) : 2.048
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2VK5 COMPLIES WITH FORMAT V. 3.20, 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-34803.
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 : ID14-1
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 : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 281317
REMARK 200 RESOLUTION RANGE HIGH (A) : 0.97
REMARK 200 RESOLUTION RANGE LOW (A) : 20.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 4.6
REMARK 200 R MERGE (I) : 0.07
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.60
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.1
REMARK 200 R MERGE FOR SHELL (I) : 0.33
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 1SLL
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 34
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.9
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 48.44600
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.40400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.50950
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.40400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.44600
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.50950
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 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 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER;
REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 480 I=INSERTION CODE):
REMARK 480 M RES CSSEQI ATOMS
REMARK 480 GLU A1313 OE1 OE2
REMARK 480 VAL A1344 CG1
REMARK 480 GLU A1632 OE2
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 N VAL A 1243 - O HOH A 2241 1.86
REMARK 500 NE ARG A 1286 - O HOH A 2302 1.87
REMARK 500 CZ ARG A 1286 - O HOH A 2302 1.56
REMARK 500 NH1 ARG A 1286 - O HOH A 2302 1.47
REMARK 500 OD1 ASP A 1296 - O HOH A 2329 1.94
REMARK 500 C MET A 1318 - O HOH A 2373 1.92
REMARK 500 N ASP A 1319 - O HOH A 2373 1.88
REMARK 500 O TYR A 1320 - O HOH A 2329 2.14
REMARK 500 N VAL A 1326 - O HOH A 2386 2.20
REMARK 500 CG1 ILE A 1340 - O HOH A 2409 1.07
REMARK 500 CD1 ILE A 1340 - O HOH A 2409 2.08
REMARK 500 N LEU A 1342 - O HOH A 2410 1.88
REMARK 500 CA LEU A 1342 - O HOH A 2410 0.89
REMARK 500 C LEU A 1342 - O HOH A 2410 1.85
REMARK 500 CB LEU A 1342 - O HOH A 2410 2.18
REMARK 500 N THR A 1345 - O HOH A 2412 1.91
REMARK 500 CA THR A 1345 - O HOH A 2412 0.96
REMARK 500 C THR A 1345 - O HOH A 2412 2.08
REMARK 500 CB THR A 1345 - O HOH A 2412 2.17
REMARK 500 CB ASN A 1364 - O HOH A 2442 1.67
REMARK 500 CG ASN A 1364 - O HOH A 2442 1.54
REMARK 500 OD1 ASN A 1364 - O HOH A 2442 1.48
REMARK 500 CG LYS A 1368 - O HOH A 2458 2.04
REMARK 500 CA SER A 1376 - O HOH A 2473 2.09
REMARK 500 CB SER A 1376 - O HOH A 2473 1.42
REMARK 500 N SER A 1429 - O HOH A 2572 1.98
REMARK 500 CA SER A 1429 - O HOH A 2572 1.04
REMARK 500 C SER A 1429 - O HOH A 2572 2.17
REMARK 500 CB SER A 1429 - O HOH A 2572 2.18
REMARK 500 OD1 ASN A 1432 - O HOH A 2575 1.27
REMARK 500 C SER A 1444 - O HOH A 2599 2.03
REMARK 500 N GLU A 1445 - O HOH A 2599 1.05
REMARK 500 CA GLU A 1445 - O HOH A 2599 2.19
REMARK 500 OE2 GLU A 1445 - O HOH A 2606 1.35
REMARK 500 CB GLN A 1447 - O HOH A 2612 1.49
REMARK 500 CG GLN A 1447 - O HOH A 2612 1.96
REMARK 500 CG LYS A 1455 - O HOH A 2622 1.39
REMARK 500 CE LYS A 1455 - O HOH A 2624 1.75
REMARK 500 CB ASP A 1456 - O HOH A 2626 1.90
REMARK 500 CB LYS A 1459 - O HOH A 2630 1.36
REMARK 500 CG LYS A 1459 - O HOH A 2630 1.84
REMARK 500 CD LYS A 1459 - O HOH A 2632 1.63
REMARK 500 N LEU A 1461 - O HOH A 2634 2.06
REMARK 500 CA LEU A 1461 - O HOH A 2634 1.04
REMARK 500 C LEU A 1461 - O HOH A 2634 2.14
REMARK 500 CB LEU A 1461 - O HOH A 2634 2.13
REMARK 500 CB ARG A 1467 - O HOH A 2639 1.14
REMARK 500 CG ARG A 1467 - O HOH A 2639 1.39
REMARK 500 CD ARG A 1467 - O HOH A 2639 1.76
REMARK 500 N VAL A 1482 - O HOH A 2661 1.92
REMARK 500
REMARK 500 THIS ENTRY HAS 152 CLOSE CONTACTS
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
REMARK 500 O HOH A 2136 O HOH A 3024 2655 2.09
REMARK 500 O HOH A 2401 O HOH A 3008 3755 1.81
REMARK 500 O HOH A 2452 O HOH A 2881 3755 1.72
REMARK 500 O HOH A 2563 O HOH A 2724 4455 1.43
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A1676 CD GLU A1676 OE1 0.068
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 A1253 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES
REMARK 500 ASP A1283 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES
REMARK 500 ARG A1286 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 ARG A1286 NH1 - CZ - NH2 ANGL. DEV. = 7.8 DEGREES
REMARK 500 ARG A1302 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 ASP A1335 CA - CB - CG ANGL. DEV. = 16.3 DEGREES
REMARK 500 ASP A1335 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 ASP A1366 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES
REMARK 500 ARG A1384 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 LEU A1433 CB - CG - CD2 ANGL. DEV. = 15.1 DEGREES
REMARK 500 ASP A1456 CB - CG - OD1 ANGL. DEV. = -8.3 DEGREES
REMARK 500 ARG A1613 CD - NE - CZ ANGL. DEV. = 40.2 DEGREES
REMARK 500 ARG A1613 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 TYR A1655 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 TYR A1655 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 GLU A1676 CG - CD - OE1 ANGL. DEV. = 13.9 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 A1267 74.84 77.27
REMARK 500 ASN A1294 48.91 -90.50
REMARK 500 ASN A1295 -178.88 -170.50
REMARK 500 ASP A1328 84.75 75.18
REMARK 500 LYS A1350 -4.36 83.86
REMARK 500 ASP A1414 -159.98 -171.38
REMARK 500 LYS A1459 -68.55 -92.93
REMARK 500 THR A1538 -122.13 -125.70
REMARK 500 TYR A1587 67.03 79.05
REMARK 500 ALA A1654 -114.44 -121.47
REMARK 500 SER A1675 27.90 -158.57
REMARK 500 GLU A1676 -97.20 -119.91
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 CA A 10 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2710 O
REMARK 620 2 TRP A1573 O 80.0
REMARK 620 3 ASP A1515 O 86.0 162.1
REMARK 620 4 HOH A2713 O 95.4 89.7 102.6
REMARK 620 5 HOH A2704 O 95.0 84.2 86.1 166.9
REMARK 620 6 HOH A2708 O 169.1 108.9 84.0 91.0 80.1
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 17 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2330 O
REMARK 620 2 ASP A1296 OD1 80.2
REMARK 620 3 HOH A2329 O 105.9 56.5
REMARK 620 4 ASP A1298 OD1 146.9 104.1 103.5
REMARK 620 5 ASP A1319 OD1 88.7 167.1 133.9 81.7
REMARK 620 6 TYR A1320 O 74.0 100.6 61.5 135.0 82.3
REMARK 620 7 HOH A2332 O 71.5 86.2 141.9 76.0 84.1 143.1
REMARK 620 8 HOH A2384 O 143.9 85.3 40.3 68.8 107.5 76.5 140.4
REMARK 620 N 1 2 3 4 5 6 7
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 GOL A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 6
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 10
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 17
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2BF6 RELATED DB: PDB
REMARK 900 ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE
REMARK 900 NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA
REMARK 900 -SIALIC ACID (NEU5AC).
REMARK 900 RELATED ID: 2VK7 RELATED DB: PDB
REMARK 900 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE
REMARK 900 AND ITS CATALYTIC INTERMEDIATES
REMARK 900 RELATED ID: 2VK6 RELATED DB: PDB
REMARK 900 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE
REMARK 900 AND ITS CATALYTIC INTERMEDIATES
DBREF 2VK5 A 1243 1694 UNP Q59310 Q59310_CLOPE 243 694
SEQADV 2VK5 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 GOL A 1 6
HET GOL A 6 6
HET CA A 10 1
HET CA A 17 1
HETNAM GOL GLYCEROL
HETNAM CA CALCIUM ION
FORMUL 2 GOL 2(C3 H8 O3)
FORMUL 3 CA 2(CA 2+)
FORMUL 4 HOH *1030(H2 O)
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 1473 LYS A 1477 5 5
HELIX 4 4 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 TYR A1670 -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 ARG A1339 PHE A1347 -1 O ILE A1340 N SER A1436
SHEET 4 AC 5 SER A1325 ASP A1334 -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 A 10 O HOH A2710 1555 1555 2.49
LINK CA CA A 10 O TRP A1573 1555 1555 2.56
LINK CA CA A 10 O ASP A1515 1555 1555 2.46
LINK CA CA A 10 O HOH A2713 1555 1555 2.13
LINK CA CA A 10 O HOH A2704 1555 1555 2.63
LINK CA CA A 10 O HOH A2708 1555 1555 2.56
LINK CA CA A 17 O HOH A2329 1555 1555 1.50
LINK CA CA A 17 OD1 ASP A1296 1555 1555 2.31
LINK CA CA A 17 OD1 ASP A1298 1555 1555 2.41
LINK CA CA A 17 OD1 ASP A1319 1555 1555 2.35
LINK CA CA A 17 O TYR A1320 1555 1555 2.40
LINK CA CA A 17 O HOH A2332 1555 1555 2.48
LINK CA CA A 17 O HOH A2384 1555 1555 2.50
LINK CA CA A 17 O HOH A2330 1555 1555 2.49
CISPEP 1 ALA A 1292 PRO A 1293 0 7.86
SITE 1 AC1 9 LYS A1551 GLU A1578 TYR A1631 GLU A1639
SITE 2 AC1 9 HOH A2225 HOH A2226 HOH A2227 HOH A2228
SITE 3 AC1 9 HOH A2797
SITE 1 AC2 9 GLU A1578 LYS A1579 ASP A1580 THR A1581
SITE 2 AC2 9 ASN A1582 GLU A1639 HOH A2233 HOH A2235
SITE 3 AC2 9 HOH A2814
SITE 1 AC3 6 ASP A1515 TRP A1573 HOH A2704 HOH A2708
SITE 2 AC3 6 HOH A2710 HOH A2713
SITE 1 AC4 8 ASP A1296 ASP A1298 ASP A1319 TYR A1320
SITE 2 AC4 8 HOH A2329 HOH A2330 HOH A2332 HOH A2384
CRYST1 96.892 69.019 72.808 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 0.010321 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014489 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013735 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
