HEADER HYDROLASE 17-DEC-07 2VK5 TITLE THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS TITLE 2 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 6 13-DEC-23 2VK5 1 REMARK LINK REVDAT 5 14-JUN-17 2VK5 1 REMARK 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) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 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 : 3524 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034803. 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 CCD 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) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 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 : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 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: 1SLL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 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; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 1313 OE1 OE2 REMARK 480 VAL A 1344 CG1 REMARK 480 GLU A 1632 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 CA GLN A 1541 O HOH A 2758 0.76 REMARK 500 CA THR A 1508 O HOH A 2697 0.83 REMARK 500 CD1 LEU A 1433 O HOH A 2695 0.85 REMARK 500 CA VAL A 1482 O HOH A 2661 0.85 REMARK 500 CA LEU A 1342 O HOH A 2410 0.89 REMARK 500 CA THR A 1345 O HOH A 2412 0.96 REMARK 500 O HOH A 2387 O HOH A 2389 1.00 REMARK 500 O HOH A 2414 O HOH A 2415 1.01 REMARK 500 CA ILE A 1681 O HOH A 3002 1.02 REMARK 500 CA LEU A 1461 O HOH A 2634 1.04 REMARK 500 CA SER A 1429 O HOH A 2572 1.04 REMARK 500 N GLU A 1445 O HOH A 2599 1.05 REMARK 500 CB TYR A 1652 O HOH A 2943 1.06 REMARK 500 CA SER A 1558 O HOH A 2778 1.06 REMARK 500 CG1 ILE A 1340 O HOH A 2409 1.07 REMARK 500 OD1 ASP A 1291 O HOH A 2311 1.09 REMARK 500 CB ARG A 1467 O HOH A 2639 1.14 REMARK 500 CB SER A 1662 O HOH A 2952 1.14 REMARK 500 O HOH A 2554 O HOH A 2616 1.15 REMARK 500 CA ASN A 1594 O HOH A 2827 1.16 REMARK 500 O HOH A 2553 O HOH A 2556 1.19 REMARK 500 CE LYS A 1602 O HOH A 2857 1.20 REMARK 500 O HOH A 2454 O HOH A 2458 1.24 REMARK 500 OD1 ASP A 1291 O HOH A 2318 1.25 REMARK 500 OD1 ASN A 1432 O HOH A 2575 1.27 REMARK 500 O HOH A 2011 O HOH A 2495 1.30 REMARK 500 CB LYS A 1598 O HOH A 2843 1.30 REMARK 500 O HOH A 2881 O HOH A 2882 1.30 REMARK 500 OE2 GLU A 1632 O HOH A 2897 1.31 REMARK 500 O HOH A 2786 O HOH A 2790 1.31 REMARK 500 O HOH A 2662 O HOH A 3006 1.33 REMARK 500 CG LYS A 1602 O HOH A 2883 1.34 REMARK 500 OE2 GLU A 1445 O HOH A 2606 1.35 REMARK 500 CB LYS A 1459 O HOH A 2630 1.36 REMARK 500 OE2 GLU A 1313 O HOH A 2357 1.38 REMARK 500 CG LYS A 1455 O HOH A 2622 1.39 REMARK 500 CG ARG A 1467 O HOH A 2639 1.39 REMARK 500 C2 GOL A 1 O HOH A 2227 1.40 REMARK 500 O HOH A 2652 O HOH A 2653 1.41 REMARK 500 O HOH A 2041 O HOH A 2963 1.41 REMARK 500 CB SER A 1376 O HOH A 2473 1.42 REMARK 500 O HOH A 2310 O HOH A 2946 1.42 REMARK 500 O HOH A 2389 O HOH A 3006 1.43 REMARK 500 O HOH A 2042 O HOH A 2554 1.44 REMARK 500 O HOH A 2897 O HOH A 2898 1.44 REMARK 500 O HOH A 2880 O HOH A 2882 1.45 REMARK 500 O HOH A 2312 O HOH A 2389 1.46 REMARK 500 NH1 ARG A 1286 O HOH A 2302 1.47 REMARK 500 O SER A 1690 O HOH A 3022 1.47 REMARK 500 OD1 ASN A 1364 O HOH A 2442 1.48 REMARK 500 REMARK 500 THIS ENTRY HAS 182 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 O HOH A 2563 O HOH A 2724 4455 1.43 REMARK 500 O HOH A 2452 O HOH A 2881 3755 1.72 REMARK 500 O HOH A 2401 O HOH A 3008 3755 1.81 REMARK 500 O HOH A 2136 O HOH A 3024 2655 2.09 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 NH1 - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A1286 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ASP A1291 CB - CG - OD1 ANGL. DEV. = 18.7 DEGREES REMARK 500 ASP A1291 CB - CG - OD2 ANGL. DEV. = -8.0 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 VAL A1344 CG1 - CB - CG2 ANGL. DEV. = -10.9 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 - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR A1655 CB - CG - CD1 ANGL. DEV. = 4.2 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 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 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2108 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A2164 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A2202 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A2208 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A2212 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2215 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A2216 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A2218 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2221 DISTANCE = 7.08 ANGSTROMS 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 ASP A1515 O REMARK 620 2 TRP A1573 O 162.1 REMARK 620 3 HOH A2704 O 86.1 84.2 REMARK 620 4 HOH A2708 O 84.0 108.9 80.1 REMARK 620 5 HOH A2710 O 86.0 80.0 95.0 169.1 REMARK 620 6 HOH A2713 O 102.6 89.7 166.9 91.0 95.4 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 ASP A1296 OD1 REMARK 620 2 ASP A1298 OD1 104.1 REMARK 620 3 ASP A1319 OD1 167.1 81.7 REMARK 620 4 TYR A1320 O 100.6 135.0 82.3 REMARK 620 5 HOH A2329 O 56.5 103.5 133.9 61.5 REMARK 620 6 HOH A2330 O 80.2 146.9 88.7 74.0 105.9 REMARK 620 7 HOH A2332 O 86.2 76.0 84.1 143.1 141.9 71.5 REMARK 620 8 HOH A2384 O 85.3 68.8 107.5 76.5 40.3 143.9 140.4 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 NANI FROM REMARK 900 CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA -SIALIC ACID (NEU5AC). REMARK 900 RELATED ID: 2VK7 RELATED DB: PDB REMARK 900 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS REMARK 900 CATALYTIC INTERMEDIATES REMARK 900 RELATED ID: 2VK6 RELATED DB: PDB REMARK 900 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS REMARK 900 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 CA 2(CA 2+) FORMUL 6 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 ASP A1515 1555 1555 2.47 LINK CA CA A 10 O TRP A1573 1555 1555 2.56 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 10 O HOH A2710 1555 1555 2.49 LINK CA CA A 10 O HOH A2713 1555 1555 2.13 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 A2329 1555 1555 1.50 LINK CA CA A 17 O HOH A2330 1555 1555 2.49 LINK CA CA A 17 O HOH A2332 1555 1555 2.48 LINK CA CA A 17 O HOH A2384 1555 1555 2.50 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