HEADER HYDROLASE 17-DEC-07 2VK6 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 5 08-MAY-24 2VK6 1 HETSYN REVDAT 4 29-JUL-20 2VK6 1 REMARK LINK SITE REVDAT 3 24-FEB-09 2VK6 1 VERSN REVDAT 2 08-APR-08 2VK6 1 JRNL REMARK REVDAT 1 22-JAN-08 2VK6 0 JRNL AUTH S.L.NEWSTEAD,J.A.POTTER,J.C.WILSON,G.XU,C.H.CHIEN,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. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 69514 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3675 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4895 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 396 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3778 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5136 ; 1.713 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 477 ; 7.061 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 188 ;36.546 ;25.745 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 664 ;11.941 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;12.044 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2911 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1701 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2609 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 342 ; 0.121 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 43 ; 0.115 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.128 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2352 ; 1.136 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3721 ; 1.700 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1639 ; 2.598 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1402 ; 3.614 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VK6 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_1290034808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 28.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 34.68500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.45000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.52300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.45000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.68500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.52300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1692 REMARK 465 ASN A 1693 REMARK 465 LYS A 1694 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLY A1691 CA C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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 2197 O HOH A 2198 2.04 REMARK 500 OE2 GLU A 1445 O HOH A 2187 2.09 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 76.78 76.86 REMARK 500 ASN A1294 46.42 -87.41 REMARK 500 ASP A1328 95.36 77.54 REMARK 500 LYS A1350 -5.10 85.83 REMARK 500 ASP A1414 -158.07 -172.31 REMARK 500 LYS A1459 -70.16 -93.60 REMARK 500 THR A1538 -122.73 -123.08 REMARK 500 TYR A1587 61.59 76.06 REMARK 500 VAL A1628 78.70 -118.70 REMARK 500 ALA A1654 -113.76 -124.20 REMARK 500 SER A1675 29.45 -157.45 REMARK 500 GLU A1676 -95.95 -123.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2691 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1296 OD1 REMARK 620 2 ASP A1298 OD1 101.9 REMARK 620 3 ASP A1319 OD1 171.5 81.7 REMARK 620 4 TYR A1320 O 101.8 133.1 80.7 REMARK 620 5 HOH A2068 O 81.7 148.2 91.1 75.1 REMARK 620 6 HOH A2070 O 87.2 76.1 86.2 144.7 72.5 REMARK 620 7 HOH A2096 O 82.4 69.9 106.1 73.9 141.3 141.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2694 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1515 O REMARK 620 2 TRP A1573 O 167.9 REMARK 620 3 HOH A2236 O 83.7 106.2 REMARK 620 4 HOH A2237 O 87.2 88.1 78.5 REMARK 620 5 HOH A2239 O 87.4 82.6 171.1 101.1 REMARK 620 6 HOH A2241 O 98.1 89.2 88.7 165.5 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2696 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2033 O REMARK 620 2 HOH A2095 O 104.4 REMARK 620 3 HOH A2167 O 114.9 110.9 REMARK 620 4 HOH A2251 O 96.4 105.6 122.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2695 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2075 O REMARK 620 2 HOH A2076 O 107.9 REMARK 620 3 HOH A2384 O 123.3 111.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2693 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2163 O REMARK 620 2 HOH A2170 O 110.4 REMARK 620 3 HOH A2387 O 131.3 115.6 REMARK 620 N 1 2 REMARK 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 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: 2VK5 RELATED DB: PDB REMARK 900 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS REMARK 900 CATALYTIC INTERMEDIATES REMARK 900 RELATED ID: 2VK7 RELATED DB: PDB REMARK 900 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS REMARK 900 CATALYTIC INTERMEDIATE DBREF 2VK6 A 1243 1694 UNP Q59310 Q59310_CLOPE 243 694 SEQADV 2VK6 SER A 1393 UNP Q59310 GLY 393 CONFLICT SEQRES 1 A 452 VAL GLU GLY ALA VAL LYS THR GLU PRO VAL ASP LEU PHE SEQRES 2 A 452 HIS PRO GLY PHE LEU ASN SER SER ASN TYR ARG ILE PRO SEQRES 3 A 452 ALA LEU PHE LYS THR LYS GLU GLY THR LEU ILE ALA SER SEQRES 4 A 452 ILE ASP ALA ARG ARG HIS GLY GLY ALA ASP ALA PRO ASN SEQRES 5 A 452 ASN ASP ILE ASP THR ALA VAL ARG ARG SER GLU ASP GLY SEQRES 6 A 452 GLY LYS THR TRP ASP GLU GLY GLN ILE ILE MET ASP TYR SEQRES 7 A 452 PRO ASP LYS SER SER VAL ILE ASP THR THR LEU ILE GLN SEQRES 8 A 452 ASP ASP GLU THR GLY ARG ILE PHE LEU LEU VAL THR HIS SEQRES 9 A 452 PHE PRO SER LYS TYR GLY PHE TRP ASN ALA GLY LEU GLY SEQRES 10 A 452 SER GLY PHE LYS ASN ILE ASP GLY LYS GLU TYR LEU CYS SEQRES 11 A 452 LEU TYR ASP SER SER GLY LYS GLU PHE THR VAL ARG GLU SEQRES 12 A 452 ASN VAL VAL TYR ASP LYS ASP SER ASN LYS THR GLU TYR SEQRES 13 A 452 THR THR ASN ALA LEU GLY ASP LEU PHE LYS ASN GLY THR SEQRES 14 A 452 LYS ILE ASP ASN ILE ASN SER SER THR ALA PRO LEU LYS SEQRES 15 A 452 ALA LYS GLY THR SER TYR ILE ASN LEU VAL TYR SER ASP SEQRES 16 A 452 ASP ASP GLY LYS THR TRP SER GLU PRO GLN ASN ILE ASN SEQRES 17 A 452 PHE GLN VAL LYS LYS ASP TRP MET LYS PHE LEU GLY ILE SEQRES 18 A 452 ALA PRO GLY ARG GLY ILE GLN ILE LYS ASN GLY GLU HIS SEQRES 19 A 452 LYS GLY ARG ILE VAL VAL PRO VAL TYR TYR THR ASN GLU SEQRES 20 A 452 LYS GLY LYS GLN SER SER ALA VAL ILE TYR SER ASP ASP SEQRES 21 A 452 SER GLY LYS ASN TRP THR ILE GLY GLU SER PRO ASN ASP SEQRES 22 A 452 ASN ARG LYS LEU GLU ASN GLY LYS ILE ILE ASN SER LYS SEQRES 23 A 452 THR LEU SER ASP ASP ALA PRO GLN LEU THR GLU CYS GLN SEQRES 24 A 452 VAL VAL GLU MET PRO ASN GLY GLN LEU LYS LEU PHE MET SEQRES 25 A 452 ARG ASN LEU SER GLY TYR LEU ASN ILE ALA THR SER PHE SEQRES 26 A 452 ASP GLY GLY ALA THR TRP ASP GLU THR VAL GLU LYS ASP SEQRES 27 A 452 THR ASN VAL LEU GLU PRO TYR CYS GLN LEU SER VAL ILE SEQRES 28 A 452 ASN TYR SER GLN LYS VAL ASP GLY LYS ASP ALA VAL ILE SEQRES 29 A 452 PHE SER ASN PRO ASN ALA ARG SER ARG SER ASN GLY THR SEQRES 30 A 452 VAL ARG ILE GLY LEU ILE ASN GLN VAL GLY THR TYR GLU SEQRES 31 A 452 ASN GLY GLU PRO LYS TYR GLU PHE ASP TRP LYS TYR ASN SEQRES 32 A 452 LYS LEU VAL LYS PRO GLY TYR TYR ALA TYR SER CYS LEU SEQRES 33 A 452 THR GLU LEU SER ASN GLY ASN ILE GLY LEU LEU TYR GLU SEQRES 34 A 452 GLY THR PRO SER GLU GLU MET SER TYR ILE GLU MET ASN SEQRES 35 A 452 LEU LYS TYR LEU GLU SER GLY ALA ASN LYS HET CA A2691 1 HET DAN A2692 20 HET MG A2693 1 HET MG A2694 1 HET MG A2695 1 HET MG A2696 1 HET PG4 A2697 13 HETNAM CA CALCIUM ION HETNAM DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID HETNAM MG MAGNESIUM ION HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN DAN NEU5AC2EN FORMUL 2 CA CA 2+ FORMUL 3 DAN C11 H17 N O8 FORMUL 4 MG 4(MG 2+) FORMUL 8 PG4 C8 H18 O5 FORMUL 9 HOH *396(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 1684 GLU A 1689 1 6 SHEET 1 AA 4 VAL A1252 PHE A1255 0 SHEET 2 AA 4 MET A1678 MET A1683 -1 O MET A1678 N LEU A1254 SHEET 3 AA 4 ILE A1666 GLU A1671 -1 O ILE A1666 N MET A1683 SHEET 4 AA 4 SER A1656 GLU A1660 -1 O CYS A1657 N LEU A1669 SHEET 1 AB 4 ASN A1264 LYS A1272 0 SHEET 2 AB 4 LEU A1278 ARG A1285 -1 O ILE A1279 N PHE A1271 SHEET 3 AB 4 ILE A1297 SER A1304 -1 O ASP A1298 N ALA A1284 SHEET 4 AB 4 GLN A1315 MET A1318 -1 O GLN A1315 N VAL A1301 SHEET 1 AC 5 GLN A1447 ASN A1448 0 SHEET 2 AC 5 TYR A1430 SER A1436 -1 O LEU A1433 N GLN A1447 SHEET 3 AC 5 ILE A1340 PHE A1347 -1 O ILE A1340 N SER A1436 SHEET 4 AC 5 SER A1325 GLN A1333 -1 O SER A1325 N PHE A1347 SHEET 5 AC 5 GLY A1466 ARG A1467 1 O GLY A1466 N LEU A1331 SHEET 1 AD 7 PHE A1362 ILE A1365 0 SHEET 2 AD 7 LYS A1368 TYR A1374 -1 O LYS A1368 N ILE A1365 SHEET 3 AD 7 GLU A1380 ARG A1384 -1 O PHE A1381 N LEU A1373 SHEET 4 AD 7 VAL A1387 TYR A1389 -1 O VAL A1387 N ARG A1384 SHEET 5 AD 7 LYS A1395 THR A1400 -1 N THR A1396 O VAL A1388 SHEET 6 AD 7 ASP A1405 LYS A1408 -1 O PHE A1407 N THR A1399 SHEET 7 AD 7 THR A1411 ASN A1415 -1 O THR A1411 N LYS A1408 SHEET 1 AE 3 PHE A1362 ILE A1365 0 SHEET 2 AE 3 LYS A1368 TYR A1374 -1 O LYS A1368 N ILE A1365 SHEET 3 AE 3 LYS A1424 ALA A1425 -1 O LYS A1424 N TYR A1374 SHEET 1 AF 3 LEU A1461 ILE A1463 0 SHEET 2 AF 3 ILE A1480 THR A1487 -1 O TYR A1485 N GLY A1462 SHEET 3 AF 3 ILE A1469 GLN A1470 -1 O ILE A1469 N VAL A1481 SHEET 1 AG 4 LEU A1461 ILE A1463 0 SHEET 2 AG 4 ILE A1480 THR A1487 -1 O TYR A1485 N GLY A1462 SHEET 3 AG 4 GLN A1493 SER A1500 -1 O SER A1494 N TYR A1486 SHEET 4 AG 4 THR A1508 ILE A1509 -1 O THR A1508 N TYR A1499 SHEET 1 AH 2 ARG A1517 LYS A1518 0 SHEET 2 AH 2 ILE A1524 ILE A1525 -1 N ILE A1525 O ARG A1517 SHEET 1 AI 4 LEU A1537 GLU A1544 0 SHEET 2 AI 4 LEU A1550 ASN A1556 -1 O LYS A1551 N VAL A1543 SHEET 3 AI 4 TYR A1560 SER A1566 -1 O ASN A1562 N MET A1554 SHEET 4 AI 4 GLU A1578 LEU A1584 -1 O GLU A1578 N ILE A1563 SHEET 1 AJ 4 SER A1591 ASN A1594 0 SHEET 2 AJ 4 ALA A1604 PRO A1610 -1 O ILE A1606 N ILE A1593 SHEET 3 AJ 4 SER A1616 THR A1630 -1 O THR A1619 N ASN A1609 SHEET 4 AJ 4 PRO A1636 TYR A1652 -1 O LYS A1637 N VAL A1628 LINK OD1 ASP A1296 CA CA A2691 1555 1555 2.35 LINK OD1 ASP A1298 CA CA A2691 1555 1555 2.45 LINK OD1 ASP A1319 CA CA A2691 1555 1555 2.39 LINK O TYR A1320 CA CA A2691 1555 1555 2.36 LINK O ASP A1515 MG MG A2694 1555 1555 2.36 LINK O TRP A1573 MG MG A2694 1555 1555 2.50 LINK O HOH A2033 MG MG A2696 2565 1555 2.84 LINK O HOH A2068 CA CA A2691 1555 1555 2.49 LINK O HOH A2070 CA CA A2691 1555 1555 2.47 LINK O HOH A2075 MG MG A2695 1555 1555 2.65 LINK O HOH A2076 MG MG A2695 1555 1555 2.77 LINK O HOH A2095 MG MG A2696 1555 1555 2.68 LINK O HOH A2096 CA CA A2691 1555 1555 2.54 LINK O HOH A2163 MG MG A2693 1555 1555 2.28 LINK O HOH A2167 MG MG A2696 1555 1555 2.74 LINK O HOH A2170 MG MG A2693 1555 1555 2.67 LINK O HOH A2236 MG MG A2694 1555 1555 2.64 LINK O HOH A2237 MG MG A2694 1555 1555 2.54 LINK O HOH A2239 MG MG A2694 1555 1555 2.37 LINK O HOH A2241 MG MG A2694 1555 1555 2.35 LINK O HOH A2251 MG MG A2696 2565 1555 2.74 LINK O HOH A2384 MG MG A2695 1555 1555 2.76 LINK O HOH A2387 MG MG A2693 1555 1555 2.76 CISPEP 1 ALA A 1292 PRO A 1293 0 7.40 CRYST1 69.370 71.046 98.900 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014075 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010111 0.00000