HEADER HYDROLASE 18-JUL-14 3WX7 TITLE CRYSTAL STRUCTURE OF COD COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITIN OLIGOSACCHARIDE DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 26-427; COMPND 5 SYNONYM: CHITIN OLIGOSACCHARIDE DEACETYLASE COD1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 670; SOURCE 4 STRAIN: KN1699; SOURCE 5 GENE: COD1, COD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS OLIGOSACCHARIDE DEACETYLACE, CARBOHYDRATE-BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.-Y.PARK,K.SUGIYAMA,T.HIRANO,T.NISHIO REVDAT 2 03-APR-19 3WX7 1 JRNL REVDAT 1 03-DEC-14 3WX7 0 JRNL AUTH T.HIRANO,K.SUGIYAMA,Y.SAKAKI,W.HAKAMATA,S.Y.PARK,T.NISHIO JRNL TITL STRUCTURE-BASED ANALYSIS OF DOMAIN FUNCTION OF CHITIN JRNL TITL 2 OLIGOSACCHARIDE DEACETYLASE FROM VIBRIO PARAHAEMOLYTICUS. JRNL REF FEBS LETT. V. 589 145 2015 JRNL REFN ISSN 1873-3468 JRNL PMID 25479092 JRNL DOI 10.1016/J.FEBSLET.2014.11.039 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 195924 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 9869 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8376 - 4.1913 0.98 6547 381 0.1597 0.1828 REMARK 3 2 4.1913 - 3.3270 1.00 6481 308 0.1533 0.1766 REMARK 3 3 3.3270 - 2.9065 1.00 6399 338 0.1743 0.2014 REMARK 3 4 2.9065 - 2.6408 1.00 6343 351 0.1787 0.2025 REMARK 3 5 2.6408 - 2.4515 1.00 6345 356 0.1853 0.1954 REMARK 3 6 2.4515 - 2.3070 1.00 6304 352 0.1755 0.2068 REMARK 3 7 2.3070 - 2.1915 1.00 6321 326 0.1702 0.1915 REMARK 3 8 2.1915 - 2.0961 1.00 6333 308 0.1695 0.1909 REMARK 3 9 2.0961 - 2.0154 1.00 6317 296 0.1677 0.1917 REMARK 3 10 2.0154 - 1.9458 1.00 6265 334 0.1678 0.1879 REMARK 3 11 1.9458 - 1.8850 1.00 6281 361 0.1760 0.2013 REMARK 3 12 1.8850 - 1.8311 1.00 6256 325 0.1771 0.2009 REMARK 3 13 1.8311 - 1.7829 1.00 6255 320 0.1716 0.1889 REMARK 3 14 1.7829 - 1.7394 1.00 6298 324 0.1744 0.2080 REMARK 3 15 1.7394 - 1.6998 1.00 6226 329 0.1765 0.2077 REMARK 3 16 1.6998 - 1.6637 1.00 6263 309 0.1728 0.2054 REMARK 3 17 1.6637 - 1.6304 0.99 6218 334 0.1684 0.2030 REMARK 3 18 1.6304 - 1.5996 0.99 6177 342 0.1741 0.1995 REMARK 3 19 1.5996 - 1.5710 0.99 6187 330 0.1724 0.1855 REMARK 3 20 1.5710 - 1.5444 0.99 6251 298 0.1755 0.1953 REMARK 3 21 1.5444 - 1.5195 0.99 6195 312 0.1736 0.2053 REMARK 3 22 1.5195 - 1.4961 0.99 6158 364 0.1788 0.1728 REMARK 3 23 1.4961 - 1.4741 0.99 6129 339 0.1882 0.2143 REMARK 3 24 1.4741 - 1.4534 0.99 6210 321 0.1964 0.2118 REMARK 3 25 1.4534 - 1.4337 0.98 6116 321 0.1994 0.2341 REMARK 3 26 1.4337 - 1.4151 0.98 6118 323 0.2052 0.2414 REMARK 3 27 1.4151 - 1.3974 0.98 6103 330 0.2107 0.2259 REMARK 3 28 1.3974 - 1.3806 0.95 5874 322 0.2186 0.2382 REMARK 3 29 1.3806 - 1.3645 0.91 5665 310 0.2268 0.2460 REMARK 3 30 1.3645 - 1.3492 0.87 5420 305 0.2289 0.2722 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.16 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 6482 REMARK 3 ANGLE : 1.082 8870 REMARK 3 CHIRALITY : 0.044 958 REMARK 3 PLANARITY : 0.006 1174 REMARK 3 DIHEDRAL : 11.454 2246 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000096905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-11; 06-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A; BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.98; 1.28275 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 195977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.349 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.21100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 10% PEG8K, 0.2M MGCL2, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 30.90950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.18900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.05300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.18900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.90950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.05300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 OD1 ASP B 44 O HOH B 1368 2.17 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 1235 O HOH B 1288 2665 2.13 REMARK 500 O HOH A 1257 O HOH B 1208 4456 2.13 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 ASP A 36 3.39 91.01 REMARK 500 GLU A 73 20.64 -142.67 REMARK 500 SER A 94 154.87 86.56 REMARK 500 GLN A 126 -76.06 -130.69 REMARK 500 TYR A 165 -3.35 71.94 REMARK 500 ASP A 186 -70.80 -153.16 REMARK 500 MET A 238 79.00 -116.55 REMARK 500 ASP B 36 4.15 91.34 REMARK 500 GLU B 73 21.70 -143.35 REMARK 500 SER B 94 155.89 86.05 REMARK 500 GLN B 126 -76.31 -131.78 REMARK 500 TYR B 165 -4.51 72.92 REMARK 500 ASP B 186 -68.35 -152.54 REMARK 500 MET B 238 71.60 -118.41 REMARK 500 MET B 302 59.75 -91.61 REMARK 500 TRP B 366 43.21 -106.26 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 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 351 O REMARK 620 2 GLY A 219 O 172.7 REMARK 620 3 HOH A1034 O 93.3 88.8 REMARK 620 4 HOH A1014 O 91.1 81.7 95.0 REMARK 620 5 HOH A1027 O 90.2 96.9 87.2 177.4 REMARK 620 6 HOH A1012 O 91.3 87.7 169.8 94.0 83.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 351 O REMARK 620 2 GLY B 219 O 173.3 REMARK 620 3 HOH B1040 O 88.3 98.1 REMARK 620 4 HOH B1049 O 94.3 87.6 89.0 REMARK 620 5 HOH B1031 O 91.5 82.0 176.4 94.6 REMARK 620 6 HOH B1016 O 91.5 87.6 83.0 169.9 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 97 NE2 REMARK 620 2 HIS B 93 NE2 100.5 REMARK 620 3 ASP B 36 OD1 100.4 90.6 REMARK 620 4 ACT B 903 OXT 145.1 95.0 110.6 REMARK 620 5 ACT B 903 O 92.9 92.1 165.8 55.2 REMARK 620 6 HOH B1189 O 87.5 170.9 92.3 75.9 83.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 NE2 REMARK 620 2 ASP A 36 OD1 96.7 REMARK 620 3 HIS A 93 NE2 101.7 90.3 REMARK 620 4 ACT A 903 OXT 146.5 112.3 94.9 REMARK 620 5 ACT A 903 O 94.8 167.7 91.9 55.4 REMARK 620 6 HOH A1131 O 88.9 90.3 169.2 75.0 85.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 905 DBREF 3WX7 A 26 427 UNP A6P4T5 A6P4T5_VIBPH 26 427 DBREF 3WX7 B 26 427 UNP A6P4T5 A6P4T5_VIBPH 26 427 SEQRES 1 A 402 THR LYS GLY THR ILE TYR LEU THR PHE ASP ASP GLY PRO SEQRES 2 A 402 ILE ASN ALA SER ILE ASP VAL ILE ASN VAL LEU ASN GLN SEQRES 3 A 402 GLU GLU VAL LYS ALA THR PHE TYR PHE ASN ALA TRP HIS SEQRES 4 A 402 LEU ASP GLY ILE GLY ASP GLU ASN GLU ASP ARG ALA LEU SEQRES 5 A 402 GLU ALA LEU LYS LEU ALA LEU ASP SER GLY HIS ILE VAL SEQRES 6 A 402 ALA ASN HIS SER TYR ASP HIS MET VAL HIS ASN CYS VAL SEQRES 7 A 402 GLU GLU PHE GLY PRO ASN SER ALA ALA GLU CYS ASN ALA SEQRES 8 A 402 THR GLY ASP HIS GLN ILE ASN SER TYR GLN ASP PRO ALA SEQRES 9 A 402 TYR ASP ALA SER MET PHE ALA GLU ASN LEU SER VAL LEU SEQRES 10 A 402 GLU LYS TYR LEU PRO ASN ILE THR SER TYR PRO ASN TYR SEQRES 11 A 402 LYS ALA ASN GLU PHE ALA ARG LEU PRO TYR THR ASN GLY SEQRES 12 A 402 TRP ARG VAL THR LYS ASP PHE LYS ALA ASP GLY LEU CYS SEQRES 13 A 402 ALA THR SER ASP ASP LEU LYS PRO TRP GLU PRO GLY TYR SEQRES 14 A 402 ALA CYS ASP THR ALA ASN PRO SER ASN SER VAL LYS ALA SEQRES 15 A 402 ALA ILE ALA VAL GLN ASN ILE LEU ALA ASN ASN GLY TYR SEQRES 16 A 402 GLN THR HIS GLY TRP ASP VAL ASP TRP ALA PRO GLU ASN SEQRES 17 A 402 TRP GLY ILE ALA MET PRO ALA ASN SER LEU THR GLU ALA SEQRES 18 A 402 GLU PRO PHE LEU GLY TYR VAL ASP SER ALA LEU ASN THR SEQRES 19 A 402 CYS ALA PRO THR THR ILE ASN PRO ILE ASN SER LYS ALA SEQRES 20 A 402 GLN GLU PHE PRO CYS GLY THR PRO LEU HIS ALA ASP LYS SEQRES 21 A 402 VAL ILE VAL LEU THR HIS GLU PHE LEU PHE GLU ASP GLY SEQRES 22 A 402 LYS ARG GLY MET GLY ALA THR GLN ASN LEU PRO LYS LEU SEQRES 23 A 402 THR LYS PHE ILE GLN LEU ALA LYS GLN ALA GLY TYR VAL SEQRES 24 A 402 PHE ASP THR MET ASP ASN TYR THR PRO ASN TRP GLN VAL SEQRES 25 A 402 GLY ASN ASN TYR SER ALA GLY ASP TYR VAL LEU HIS LEU SEQRES 26 A 402 GLY THR VAL TYR GLN ALA VAL THR SER HIS THR ALA GLN SEQRES 27 A 402 GLN ASP TRP ALA PRO SER PRO THR SER SER LEU TRP THR SEQRES 28 A 402 ASN ALA ASP PRO ALA THR ASN TRP THR GLN ASN VAL SER SEQRES 29 A 402 TYR LYS GLN GLY ASP VAL VAL THR TYR GLN GLY LEU ARG SEQRES 30 A 402 TYR LEU VAL ASN VAL PRO HIS VAL SER GLN ALA ASP TRP SEQRES 31 A 402 SER PRO SER SER GLN ASN THR LEU PHE THR ALA LEU SEQRES 1 B 402 THR LYS GLY THR ILE TYR LEU THR PHE ASP ASP GLY PRO SEQRES 2 B 402 ILE ASN ALA SER ILE ASP VAL ILE ASN VAL LEU ASN GLN SEQRES 3 B 402 GLU GLU VAL LYS ALA THR PHE TYR PHE ASN ALA TRP HIS SEQRES 4 B 402 LEU ASP GLY ILE GLY ASP GLU ASN GLU ASP ARG ALA LEU SEQRES 5 B 402 GLU ALA LEU LYS LEU ALA LEU ASP SER GLY HIS ILE VAL SEQRES 6 B 402 ALA ASN HIS SER TYR ASP HIS MET VAL HIS ASN CYS VAL SEQRES 7 B 402 GLU GLU PHE GLY PRO ASN SER ALA ALA GLU CYS ASN ALA SEQRES 8 B 402 THR GLY ASP HIS GLN ILE ASN SER TYR GLN ASP PRO ALA SEQRES 9 B 402 TYR ASP ALA SER MET PHE ALA GLU ASN LEU SER VAL LEU SEQRES 10 B 402 GLU LYS TYR LEU PRO ASN ILE THR SER TYR PRO ASN TYR SEQRES 11 B 402 LYS ALA ASN GLU PHE ALA ARG LEU PRO TYR THR ASN GLY SEQRES 12 B 402 TRP ARG VAL THR LYS ASP PHE LYS ALA ASP GLY LEU CYS SEQRES 13 B 402 ALA THR SER ASP ASP LEU LYS PRO TRP GLU PRO GLY TYR SEQRES 14 B 402 ALA CYS ASP THR ALA ASN PRO SER ASN SER VAL LYS ALA SEQRES 15 B 402 ALA ILE ALA VAL GLN ASN ILE LEU ALA ASN ASN GLY TYR SEQRES 16 B 402 GLN THR HIS GLY TRP ASP VAL ASP TRP ALA PRO GLU ASN SEQRES 17 B 402 TRP GLY ILE ALA MET PRO ALA ASN SER LEU THR GLU ALA SEQRES 18 B 402 GLU PRO PHE LEU GLY TYR VAL ASP SER ALA LEU ASN THR SEQRES 19 B 402 CYS ALA PRO THR THR ILE ASN PRO ILE ASN SER LYS ALA SEQRES 20 B 402 GLN GLU PHE PRO CYS GLY THR PRO LEU HIS ALA ASP LYS SEQRES 21 B 402 VAL ILE VAL LEU THR HIS GLU PHE LEU PHE GLU ASP GLY SEQRES 22 B 402 LYS ARG GLY MET GLY ALA THR GLN ASN LEU PRO LYS LEU SEQRES 23 B 402 THR LYS PHE ILE GLN LEU ALA LYS GLN ALA GLY TYR VAL SEQRES 24 B 402 PHE ASP THR MET ASP ASN TYR THR PRO ASN TRP GLN VAL SEQRES 25 B 402 GLY ASN ASN TYR SER ALA GLY ASP TYR VAL LEU HIS LEU SEQRES 26 B 402 GLY THR VAL TYR GLN ALA VAL THR SER HIS THR ALA GLN SEQRES 27 B 402 GLN ASP TRP ALA PRO SER PRO THR SER SER LEU TRP THR SEQRES 28 B 402 ASN ALA ASP PRO ALA THR ASN TRP THR GLN ASN VAL SER SEQRES 29 B 402 TYR LYS GLN GLY ASP VAL VAL THR TYR GLN GLY LEU ARG SEQRES 30 B 402 TYR LEU VAL ASN VAL PRO HIS VAL SER GLN ALA ASP TRP SEQRES 31 B 402 SER PRO SER SER GLN ASN THR LEU PHE THR ALA LEU HET CA A 901 1 HET ZN A 902 1 HET ACT A 903 4 HET GOL A 904 6 HET GOL A 905 6 HET CA B 901 1 HET ZN B 902 1 HET ACT B 903 4 HET GOL B 904 6 HET GOL B 905 6 HETNAM CA CALCIUM ION HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CA 2(CA 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 6 GOL 4(C3 H8 O3) FORMUL 13 HOH *1237(H2 O) HELIX 1 1 ILE A 39 GLU A 52 1 14 HELIX 2 2 ASN A 61 LEU A 65 5 5 HELIX 3 3 ARG A 75 SER A 86 1 12 HELIX 4 4 MET A 98 CYS A 102 5 5 HELIX 5 5 ASN A 109 GLY A 118 1 10 HELIX 6 6 ASP A 127 LEU A 146 1 20 HELIX 7 7 ASN A 148 TYR A 152 5 5 HELIX 8 8 SER A 202 ASN A 218 1 17 HELIX 9 9 MET A 238 LEU A 243 5 6 HELIX 10 10 GLU A 245 LEU A 257 1 13 HELIX 11 11 CYS A 260 ILE A 265 1 6 HELIX 12 12 PRO A 267 LYS A 271 5 5 HELIX 13 13 THR A 279 ALA A 283 5 5 HELIX 14 14 HIS A 291 PHE A 295 5 5 HELIX 15 15 GLY A 303 GLY A 322 1 20 HELIX 16 16 THR A 327 TYR A 331 5 5 HELIX 17 17 GLN A 412 SER A 416 5 5 HELIX 18 18 ILE B 39 GLU B 52 1 14 HELIX 19 19 ASN B 61 LEU B 65 5 5 HELIX 20 20 ARG B 75 SER B 86 1 12 HELIX 21 21 MET B 98 VAL B 103 5 6 HELIX 22 22 ASN B 109 GLY B 118 1 10 HELIX 23 23 ASP B 127 LEU B 146 1 20 HELIX 24 24 ASN B 148 TYR B 152 5 5 HELIX 25 25 SER B 202 ASN B 218 1 17 HELIX 26 26 MET B 238 LEU B 243 5 6 HELIX 27 27 GLU B 245 LEU B 257 1 13 HELIX 28 28 CYS B 260 ILE B 265 1 6 HELIX 29 29 PRO B 267 LYS B 271 5 5 HELIX 30 30 THR B 279 ALA B 283 5 5 HELIX 31 31 PHE B 293 PHE B 295 5 3 HELIX 32 32 GLY B 303 ALA B 321 1 19 HELIX 33 33 THR B 327 TYR B 331 5 5 HELIX 34 34 GLN B 412 SER B 416 5 5 SHEET 1 A 5 ILE A 89 ASN A 92 0 SHEET 2 A 5 THR A 57 PHE A 60 1 N PHE A 58 O ILE A 89 SHEET 3 A 5 GLY A 28 ASP A 35 1 N PHE A 34 O TYR A 59 SHEET 4 A 5 LYS A 285 THR A 290 1 O THR A 290 N ASP A 35 SHEET 5 A 5 VAL A 227 ASP A 228 1 N VAL A 227 O LEU A 289 SHEET 1 B 4 ILE A 89 ASN A 92 0 SHEET 2 B 4 THR A 57 PHE A 60 1 N PHE A 58 O ILE A 89 SHEET 3 B 4 GLY A 28 ASP A 35 1 N PHE A 34 O TYR A 59 SHEET 4 B 4 TYR A 323 ASP A 326 1 O VAL A 324 N ILE A 30 SHEET 1 C 2 PHE A 160 ALA A 161 0 SHEET 2 C 2 GLN A 221 THR A 222 1 O GLN A 221 N ALA A 161 SHEET 1 D 2 TRP A 169 THR A 172 0 SHEET 2 D 2 PHE A 175 ALA A 177 -1 O PHE A 175 N VAL A 171 SHEET 1 E 2 ASP A 297 GLY A 298 0 SHEET 2 E 2 GLY A 301 MET A 302 -1 O GLY A 301 N GLY A 298 SHEET 1 F 2 ASN A 340 TYR A 341 0 SHEET 2 F 2 HIS A 360 THR A 361 -1 O HIS A 360 N TYR A 341 SHEET 1 G 3 TYR A 346 HIS A 349 0 SHEET 2 G 3 THR A 352 ALA A 356 -1 O TYR A 354 N VAL A 347 SHEET 3 G 3 TRP A 375 ASN A 377 -1 O THR A 376 N GLN A 355 SHEET 1 H 2 SER A 389 TYR A 390 0 SHEET 2 H 2 HIS A 409 VAL A 410 -1 O HIS A 409 N TYR A 390 SHEET 1 I 3 VAL A 395 TYR A 398 0 SHEET 2 I 3 LEU A 401 VAL A 405 -1 O LEU A 401 N TYR A 398 SHEET 3 I 3 PHE A 424 ALA A 426 -1 O THR A 425 N LEU A 404 SHEET 1 J 5 ILE B 89 ASN B 92 0 SHEET 2 J 5 THR B 57 PHE B 60 1 N PHE B 58 O ALA B 91 SHEET 3 J 5 GLY B 28 ASP B 35 1 N PHE B 34 O TYR B 59 SHEET 4 J 5 LYS B 285 HIS B 291 1 O THR B 290 N ASP B 35 SHEET 5 J 5 VAL B 227 ASP B 228 1 N VAL B 227 O LEU B 289 SHEET 1 K 4 ILE B 89 ASN B 92 0 SHEET 2 K 4 THR B 57 PHE B 60 1 N PHE B 58 O ALA B 91 SHEET 3 K 4 GLY B 28 ASP B 35 1 N PHE B 34 O TYR B 59 SHEET 4 K 4 TYR B 323 ASP B 326 1 O VAL B 324 N ILE B 30 SHEET 1 L 2 PHE B 160 ALA B 161 0 SHEET 2 L 2 GLN B 221 THR B 222 1 O GLN B 221 N ALA B 161 SHEET 1 M 2 TRP B 169 THR B 172 0 SHEET 2 M 2 PHE B 175 ALA B 177 -1 O ALA B 177 N TRP B 169 SHEET 1 N 2 ASP B 297 GLY B 298 0 SHEET 2 N 2 GLY B 301 MET B 302 -1 O GLY B 301 N GLY B 298 SHEET 1 O 2 ASN B 340 TYR B 341 0 SHEET 2 O 2 HIS B 360 THR B 361 -1 O HIS B 360 N TYR B 341 SHEET 1 P 3 TYR B 346 HIS B 349 0 SHEET 2 P 3 THR B 352 ALA B 356 -1 O TYR B 354 N VAL B 347 SHEET 3 P 3 TRP B 375 ASN B 377 -1 O THR B 376 N GLN B 355 SHEET 1 Q 2 SER B 389 TYR B 390 0 SHEET 2 Q 2 HIS B 409 VAL B 410 -1 O HIS B 409 N TYR B 390 SHEET 1 R 3 VAL B 395 TYR B 398 0 SHEET 2 R 3 LEU B 401 VAL B 405 -1 O TYR B 403 N VAL B 396 SHEET 3 R 3 PHE B 424 ALA B 426 -1 O THR B 425 N LEU B 404 SSBOND 1 CYS A 102 CYS A 114 1555 1555 2.03 SSBOND 2 CYS A 181 CYS A 196 1555 1555 2.03 SSBOND 3 CYS A 260 CYS A 277 1555 1555 2.04 SSBOND 4 CYS B 102 CYS B 114 1555 1555 2.03 SSBOND 5 CYS B 181 CYS B 196 1555 1555 2.03 SSBOND 6 CYS B 260 CYS B 277 1555 1555 2.05 LINK O GLY A 351 CA CA A 901 1555 1555 2.06 LINK O GLY B 351 CA CA B 901 1555 1555 2.07 LINK O GLY B 219 CA CA B 901 1555 1555 2.08 LINK O GLY A 219 CA CA A 901 1555 1555 2.08 LINK NE2 HIS B 97 ZN ZN B 902 1555 1555 2.14 LINK NE2 HIS A 97 ZN ZN A 902 1555 1555 2.15 LINK NE2 HIS B 93 ZN ZN B 902 1555 1555 2.18 LINK OD1 ASP B 36 ZN ZN B 902 1555 1555 2.18 LINK OD1 ASP A 36 ZN ZN A 902 1555 1555 2.19 LINK NE2 HIS A 93 ZN ZN A 902 1555 1555 2.20 LINK ZN ZN B 902 OXT ACT B 903 1555 1555 2.25 LINK ZN ZN A 902 OXT ACT A 903 1555 1555 2.25 LINK ZN ZN B 902 O ACT B 903 1555 1555 2.40 LINK ZN ZN A 902 O ACT A 903 1555 1555 2.42 LINK CA CA A 901 O HOH A1034 1555 1555 2.09 LINK CA CA A 901 O HOH A1014 1555 1555 2.09 LINK CA CA B 901 O HOH B1040 1555 1555 2.11 LINK CA CA B 901 O HOH B1049 1555 1555 2.11 LINK CA CA A 901 O HOH A1027 1555 1555 2.12 LINK CA CA B 901 O HOH B1031 1555 1555 2.12 LINK CA CA A 901 O HOH A1012 1555 1555 2.13 LINK CA CA B 901 O HOH B1016 1555 1555 2.15 LINK ZN ZN A 902 O HOH A1131 1555 1555 2.32 LINK ZN ZN B 902 O HOH B1189 1555 1555 2.40 CISPEP 1 GLY A 37 PRO A 38 0 0.62 CISPEP 2 ASN A 266 PRO A 267 0 1.80 CISPEP 3 GLY B 37 PRO B 38 0 0.11 CISPEP 4 ASN B 266 PRO B 267 0 2.92 SITE 1 AC1 6 GLY A 219 GLY A 351 HOH A1012 HOH A1014 SITE 2 AC1 6 HOH A1027 HOH A1034 SITE 1 AC2 5 ASP A 36 HIS A 93 HIS A 97 ACT A 903 SITE 2 AC2 5 HOH A1131 SITE 1 AC3 10 ASP A 35 ASP A 36 HIS A 93 HIS A 97 SITE 2 AC3 10 PRO A 164 TYR A 165 TRP A 225 HIS A 291 SITE 3 AC3 10 ZN A 902 HOH A1131 SITE 1 AC4 5 PRO A 333 ASP A 345 TYR A 346 HOH A1025 SITE 2 AC4 5 HOH A1266 SITE 1 AC5 10 ASN A 383 TRP A 384 THR A 397 TYR A 398 SITE 2 AC5 10 HOH A1303 HOH A1307 HOH A1356 THR B 150 SITE 3 AC5 10 SER B 151 PRO B 153 SITE 1 AC6 6 GLY B 219 GLY B 351 HOH B1016 HOH B1031 SITE 2 AC6 6 HOH B1040 HOH B1049 SITE 1 AC7 5 ASP B 36 HIS B 93 HIS B 97 ACT B 903 SITE 2 AC7 5 HOH B1189 SITE 1 AC8 10 ASP B 35 ASP B 36 HIS B 93 HIS B 97 SITE 2 AC8 10 PRO B 164 TYR B 165 TRP B 225 HIS B 291 SITE 3 AC8 10 ZN B 902 HOH B1189 SITE 1 AC9 5 PRO B 333 ASP B 345 TYR B 346 HOH B1045 SITE 2 AC9 5 HOH B1245 SITE 1 BC1 9 THR A 150 SER A 151 PRO A 153 ASN B 383 SITE 2 BC1 9 TRP B 384 THR B 397 TYR B 398 HOH B1439 SITE 3 BC1 9 HOH B1457 CRYST1 61.819 104.106 140.378 90.00 90.00 90.00 P 21 21 21 8 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 0.016176 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007124 0.00000