HEADER HYDROLASE 10-DEC-13 4NY2 TITLE STRUCTURE OF VIBRIO CHOLERAE CHITIN DE-N-ACETYLASE IN COMPLEX WITH TITLE 2 ACETATE ION (ACT) IN P 21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEACETYLASE DA1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 23-427; COMPND 5 EC: 3.5.1.41; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 1095658; SOURCE 4 GENE: DEAA, VCNHCC010F_001593; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS (BETA/ALPHA)7, CARBOHYDRATE ESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.ALBESA-JOVE,E.ANDRES,X.BIARNES,A.PLANAS,M.E.GUERIN REVDAT 3 08-NOV-23 4NY2 1 REMARK SEQADV LINK REVDAT 2 26-NOV-14 4NY2 1 TITLE REVDAT 1 13-AUG-14 4NY2 0 JRNL AUTH E.ANDRES,D.ALBESA-JOVE,X.BIARNES,B.M.MOERSCHBACHER, JRNL AUTH 2 M.E.GUERIN,A.PLANAS JRNL TITL STRUCTURAL BASIS OF CHITIN OLIGOSACCHARIDE DEACETYLATION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 6882 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 24810719 JRNL DOI 10.1002/ANIE.201400220 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 76429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3840 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 29.5081 - 5.6230 1.00 2742 160 0.1620 0.1924 REMARK 3 2 5.6230 - 4.4682 1.00 2752 129 0.1248 0.1220 REMARK 3 3 4.4682 - 3.9048 0.99 2718 134 0.1101 0.1357 REMARK 3 4 3.9048 - 3.5484 1.00 2729 148 0.1264 0.1598 REMARK 3 5 3.5484 - 3.2945 1.00 2659 165 0.1326 0.1938 REMARK 3 6 3.2945 - 3.1004 1.00 2709 149 0.1437 0.1762 REMARK 3 7 3.1004 - 2.9453 1.00 2732 136 0.1398 0.1687 REMARK 3 8 2.9453 - 2.8172 1.00 2685 160 0.1357 0.1683 REMARK 3 9 2.8172 - 2.7088 1.00 2735 134 0.1381 0.1968 REMARK 3 10 2.7088 - 2.6154 1.00 2705 152 0.1355 0.1859 REMARK 3 11 2.6154 - 2.5337 1.00 2721 136 0.1347 0.1826 REMARK 3 12 2.5337 - 2.4613 1.00 2706 128 0.1402 0.1759 REMARK 3 13 2.4613 - 2.3965 1.00 2708 134 0.1469 0.2054 REMARK 3 14 2.3965 - 2.3381 1.00 2722 148 0.1473 0.2379 REMARK 3 15 2.3381 - 2.2850 1.00 2661 159 0.1506 0.2029 REMARK 3 16 2.2850 - 2.2363 1.00 2675 169 0.1580 0.2127 REMARK 3 17 2.2363 - 2.1916 1.00 2729 139 0.1499 0.1945 REMARK 3 18 2.1916 - 2.1503 1.00 2682 151 0.1548 0.1736 REMARK 3 19 2.1503 - 2.1119 1.00 2701 139 0.1601 0.1975 REMARK 3 20 2.1119 - 2.0761 1.00 2740 126 0.1756 0.2479 REMARK 3 21 2.0761 - 2.0426 1.00 2686 137 0.1850 0.2244 REMARK 3 22 2.0426 - 2.0112 1.00 2716 150 0.1923 0.2286 REMARK 3 23 2.0112 - 1.9816 1.00 2695 134 0.1998 0.2358 REMARK 3 24 1.9816 - 1.9537 1.00 2707 138 0.2158 0.2555 REMARK 3 25 1.9537 - 1.9273 1.00 2703 118 0.2263 0.2590 REMARK 3 26 1.9273 - 1.9023 1.00 2720 158 0.2288 0.3025 REMARK 3 27 1.9023 - 1.8785 0.81 2151 109 0.2419 0.2639 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 6619 REMARK 3 ANGLE : 1.113 9045 REMARK 3 CHIRALITY : 0.067 971 REMARK 3 PLANARITY : 0.006 1186 REMARK 3 DIHEDRAL : 12.908 2334 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 4NY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.879 REMARK 200 RESOLUTION RANGE LOW (A) : 29.505 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.96 REMARK 200 R MERGE FOR SHELL (I) : 0.51300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2C1I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80MM MES PH 6.5, 0.16M CA(OAC)2, 14.4% REMARK 280 (W/V) PEG 8000, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 56.27000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 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 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 MET A 26 REMARK 465 ASN A 27 REMARK 465 SER A 28 REMARK 465 ARG A 434 REMARK 465 ARG A 435 REMARK 465 GLN A 436 REMARK 465 TRP A 437 REMARK 465 SER A 438 REMARK 465 HIS A 439 REMARK 465 PRO A 440 REMARK 465 GLN A 441 REMARK 465 PHE A 442 REMARK 465 GLU A 443 REMARK 465 LYS A 444 REMARK 465 MET B 26 REMARK 465 ASN B 27 REMARK 465 LEU B 433 REMARK 465 ARG B 434 REMARK 465 ARG B 435 REMARK 465 GLN B 436 REMARK 465 TRP B 437 REMARK 465 SER B 438 REMARK 465 HIS B 439 REMARK 465 PRO B 440 REMARK 465 GLN B 441 REMARK 465 PHE B 442 REMARK 465 GLU B 443 REMARK 465 LYS B 444 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 THR A 29 N CA CB OG1 CG2 REMARK 470 GLU A 108 CG CD OE1 OE2 REMARK 470 ASN A 190 CG OD1 ND2 REMARK 470 LEU A 433 CG CD1 CD2 REMARK 470 SER B 28 N CA CB OG REMARK 470 THR B 29 OG1 CG2 REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 GLU B 109 CD OE1 OE2 REMARK 470 LYS B 343 CE NZ REMARK 470 GLU B 432 CA C O CB CG CD OE1 REMARK 470 GLU B 432 OE2 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 40 0.38 96.44 REMARK 500 GLU A 77 16.09 -140.47 REMARK 500 SER A 98 156.39 87.36 REMARK 500 GLN A 130 -80.39 -125.62 REMARK 500 TYR A 169 -7.26 75.03 REMARK 500 ASN A 190 -56.99 -155.67 REMARK 500 TRP A 370 55.29 -115.15 REMARK 500 PRO A 384 41.07 -83.73 REMARK 500 TRP A 419 48.46 -104.73 REMARK 500 ASP B 40 4.81 91.09 REMARK 500 GLU B 77 19.76 -146.68 REMARK 500 SER B 98 154.36 89.44 REMARK 500 GLN B 130 -77.41 -129.73 REMARK 500 TYR B 169 -2.93 73.18 REMARK 500 ASN B 190 -75.17 -158.86 REMARK 500 TRP B 370 43.33 -101.86 REMARK 500 PRO B 384 43.59 -80.86 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD1 REMARK 620 2 HIS A 97 NE2 90.2 REMARK 620 3 HIS A 101 NE2 98.7 97.7 REMARK 620 4 ACT A 503 OXT 105.3 88.3 155.3 REMARK 620 5 ACT A 503 O 164.4 92.4 96.2 59.5 REMARK 620 6 HOH A 724 O 89.0 174.0 88.3 86.2 86.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 223 O REMARK 620 2 GLY A 355 O 174.1 REMARK 620 3 HOH A 604 O 84.3 97.6 REMARK 620 4 HOH A 605 O 95.5 90.4 78.1 REMARK 620 5 HOH A 608 O 82.8 91.4 95.3 173.3 REMARK 620 6 HOH A 653 O 86.6 93.2 160.9 86.1 100.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 40 OD1 REMARK 620 2 HIS B 97 NE2 85.9 REMARK 620 3 HIS B 101 NE2 96.8 99.4 REMARK 620 4 ACT B 503 O 164.7 95.3 98.0 REMARK 620 5 ACT B 503 OXT 107.1 90.6 154.7 57.7 REMARK 620 6 HOH B 801 O 91.4 173.3 87.0 85.7 84.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 223 O REMARK 620 2 GLY B 355 O 171.0 REMARK 620 3 HOH B 603 O 97.0 91.2 REMARK 620 4 HOH B 604 O 81.6 90.6 175.1 REMARK 620 5 HOH B 606 O 81.5 95.2 87.1 97.3 REMARK 620 6 HOH B 611 O 88.3 96.8 80.6 94.6 163.0 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NYU RELATED DB: PDB REMARK 900 RELATED ID: 4NYY RELATED DB: PDB REMARK 900 RELATED ID: 4NZ1 RELATED DB: PDB REMARK 900 RELATED ID: 4NZ3 RELATED DB: PDB REMARK 900 RELATED ID: 4NZ4 RELATED DB: PDB REMARK 900 RELATED ID: 4NZ5 RELATED DB: PDB DBREF 4NY2 A 27 431 UNP M7M1G8 M7M1G8_VIBCL 23 427 DBREF 4NY2 B 27 431 UNP M7M1G8 M7M1G8_VIBCL 23 427 SEQADV 4NY2 MET A 26 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLU A 432 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 LEU A 433 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 ARG A 434 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 ARG A 435 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLN A 436 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 TRP A 437 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 SER A 438 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 HIS A 439 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 PRO A 440 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLN A 441 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 PHE A 442 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLU A 443 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 LYS A 444 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 MET B 26 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLU B 432 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 LEU B 433 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 ARG B 434 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 ARG B 435 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLN B 436 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 TRP B 437 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 SER B 438 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 HIS B 439 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 PRO B 440 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLN B 441 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 PHE B 442 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 GLU B 443 UNP M7M1G8 EXPRESSION TAG SEQADV 4NY2 LYS B 444 UNP M7M1G8 EXPRESSION TAG SEQRES 1 A 419 MET ASN SER THR PRO LYS GLY THR ILE TYR LEU THR PHE SEQRES 2 A 419 ASP ASP GLY PRO VAL ASN ALA SER VAL GLU VAL ILE LYS SEQRES 3 A 419 VAL LEU ASN GLN GLY GLY VAL LYS ALA THR PHE TYR PHE SEQRES 4 A 419 ASN ALA TRP HIS LEU ASP GLY ILE GLY ASP GLU ASN GLU SEQRES 5 A 419 ASP ARG ALA LEU GLU ALA LEU LYS LEU ALA LEU ASP SER SEQRES 6 A 419 GLY HIS ILE VAL GLY ASN HIS SER TYR ASP HIS MET ILE SEQRES 7 A 419 HIS ASN CYS VAL GLU GLU PHE GLY PRO THR SER GLY ALA SEQRES 8 A 419 ASP CYS ASN ALA THR GLY ASN HIS GLN ILE HIS SER TYR SEQRES 9 A 419 GLN ASP PRO VAL ARG ASP ALA ALA SER PHE GLU GLN ASN SEQRES 10 A 419 LEU ILE THR LEU GLU LYS TYR LEU PRO THR ILE ARG SER SEQRES 11 A 419 TYR PRO ASN TYR LYS GLY TYR GLU LEU ALA ARG LEU PRO SEQRES 12 A 419 TYR THR ASN GLY TRP ARG VAL THR LYS HIS PHE GLN ALA SEQRES 13 A 419 ASP GLY LEU CYS ALA THR SER ASP ASN LEU LYS PRO TRP SEQRES 14 A 419 GLU PRO GLY TYR VAL CYS ASP PRO ALA ASN PRO SER ASN SEQRES 15 A 419 SER VAL LYS ALA SER ILE GLN VAL GLN ASN ILE LEU ALA SEQRES 16 A 419 ASN GLN GLY TYR GLN THR HIS GLY TRP ASP VAL ASP TRP SEQRES 17 A 419 ALA PRO GLU ASN TRP GLY ILE PRO MET PRO ALA ASN SER SEQRES 18 A 419 LEU THR GLU ALA VAL PRO PHE LEU ALA TYR VAL ASP LYS SEQRES 19 A 419 ALA LEU ASN SER CYS SER PRO THR THR ILE GLU PRO ILE SEQRES 20 A 419 ASN SER LYS THR GLN GLU PHE PRO CYS GLY THR PRO LEU SEQRES 21 A 419 HIS ALA ASP LYS VAL ILE VAL LEU THR HIS ASP PHE LEU SEQRES 22 A 419 PHE GLU ASP GLY LYS ARG GLY MET GLY ALA THR GLN ASN SEQRES 23 A 419 LEU PRO LYS LEU ALA GLU PHE ILE ARG ILE ALA LYS GLU SEQRES 24 A 419 ALA GLY TYR VAL PHE ASP THR MET ASP ASN TYR THR PRO SEQRES 25 A 419 ARG TRP SER VAL GLY LYS THR TYR GLN ALA GLY GLU TYR SEQRES 26 A 419 VAL LEU TYR GLN GLY VAL VAL TYR LYS ALA VAL ILE SER SEQRES 27 A 419 HIS THR ALA GLN GLN ASP TRP ALA PRO SER SER THR SER SEQRES 28 A 419 SER LEU TRP THR ASN ALA ASP PRO ALA THR ASN TRP THR SEQRES 29 A 419 LEU ASN VAL SER TYR GLU GLN GLY ASP ILE VAL ASN TYR SEQRES 30 A 419 LYS GLY LYS ARG TYR LEU VAL SER VAL PRO HIS VAL SER SEQRES 31 A 419 GLN GLN ASP TRP THR PRO ASP THR GLN ASN THR LEU PHE SEQRES 32 A 419 THR ALA LEU GLU LEU ARG ARG GLN TRP SER HIS PRO GLN SEQRES 33 A 419 PHE GLU LYS SEQRES 1 B 419 MET ASN SER THR PRO LYS GLY THR ILE TYR LEU THR PHE SEQRES 2 B 419 ASP ASP GLY PRO VAL ASN ALA SER VAL GLU VAL ILE LYS SEQRES 3 B 419 VAL LEU ASN GLN GLY GLY VAL LYS ALA THR PHE TYR PHE SEQRES 4 B 419 ASN ALA TRP HIS LEU ASP GLY ILE GLY ASP GLU ASN GLU SEQRES 5 B 419 ASP ARG ALA LEU GLU ALA LEU LYS LEU ALA LEU ASP SER SEQRES 6 B 419 GLY HIS ILE VAL GLY ASN HIS SER TYR ASP HIS MET ILE SEQRES 7 B 419 HIS ASN CYS VAL GLU GLU PHE GLY PRO THR SER GLY ALA SEQRES 8 B 419 ASP CYS ASN ALA THR GLY ASN HIS GLN ILE HIS SER TYR SEQRES 9 B 419 GLN ASP PRO VAL ARG ASP ALA ALA SER PHE GLU GLN ASN SEQRES 10 B 419 LEU ILE THR LEU GLU LYS TYR LEU PRO THR ILE ARG SER SEQRES 11 B 419 TYR PRO ASN TYR LYS GLY TYR GLU LEU ALA ARG LEU PRO SEQRES 12 B 419 TYR THR ASN GLY TRP ARG VAL THR LYS HIS PHE GLN ALA SEQRES 13 B 419 ASP GLY LEU CYS ALA THR SER ASP ASN LEU LYS PRO TRP SEQRES 14 B 419 GLU PRO GLY TYR VAL CYS ASP PRO ALA ASN PRO SER ASN SEQRES 15 B 419 SER VAL LYS ALA SER ILE GLN VAL GLN ASN ILE LEU ALA SEQRES 16 B 419 ASN GLN GLY TYR GLN THR HIS GLY TRP ASP VAL ASP TRP SEQRES 17 B 419 ALA PRO GLU ASN TRP GLY ILE PRO MET PRO ALA ASN SER SEQRES 18 B 419 LEU THR GLU ALA VAL PRO PHE LEU ALA TYR VAL ASP LYS SEQRES 19 B 419 ALA LEU ASN SER CYS SER PRO THR THR ILE GLU PRO ILE SEQRES 20 B 419 ASN SER LYS THR GLN GLU PHE PRO CYS GLY THR PRO LEU SEQRES 21 B 419 HIS ALA ASP LYS VAL ILE VAL LEU THR HIS ASP PHE LEU SEQRES 22 B 419 PHE GLU ASP GLY LYS ARG GLY MET GLY ALA THR GLN ASN SEQRES 23 B 419 LEU PRO LYS LEU ALA GLU PHE ILE ARG ILE ALA LYS GLU SEQRES 24 B 419 ALA GLY TYR VAL PHE ASP THR MET ASP ASN TYR THR PRO SEQRES 25 B 419 ARG TRP SER VAL GLY LYS THR TYR GLN ALA GLY GLU TYR SEQRES 26 B 419 VAL LEU TYR GLN GLY VAL VAL TYR LYS ALA VAL ILE SER SEQRES 27 B 419 HIS THR ALA GLN GLN ASP TRP ALA PRO SER SER THR SER SEQRES 28 B 419 SER LEU TRP THR ASN ALA ASP PRO ALA THR ASN TRP THR SEQRES 29 B 419 LEU ASN VAL SER TYR GLU GLN GLY ASP ILE VAL ASN TYR SEQRES 30 B 419 LYS GLY LYS ARG TYR LEU VAL SER VAL PRO HIS VAL SER SEQRES 31 B 419 GLN GLN ASP TRP THR PRO ASP THR GLN ASN THR LEU PHE SEQRES 32 B 419 THR ALA LEU GLU LEU ARG ARG GLN TRP SER HIS PRO GLN SEQRES 33 B 419 PHE GLU LYS HET ZN A 501 1 HET CA A 502 1 HET ACT A 503 4 HET GOL A 504 6 HET ZN B 501 1 HET CA B 502 1 HET ACT B 503 4 HET GOL B 504 6 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 CA 2(CA 2+) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 11 HOH *727(H2 O) HELIX 1 1 ALA A 45 GLY A 56 1 12 HELIX 2 2 ASN A 65 LEU A 69 5 5 HELIX 3 3 ARG A 79 SER A 90 1 12 HELIX 4 4 MET A 102 CYS A 106 5 5 HELIX 5 5 THR A 113 GLY A 122 1 10 HELIX 6 6 ASP A 131 LEU A 150 1 20 HELIX 7 7 THR A 152 TYR A 156 5 5 HELIX 8 8 SER A 206 GLN A 222 1 17 HELIX 9 9 MET A 242 LEU A 247 5 6 HELIX 10 10 GLU A 249 LEU A 261 1 13 HELIX 11 11 CYS A 264 ILE A 269 1 6 HELIX 12 12 PRO A 271 LYS A 275 5 5 HELIX 13 13 THR A 283 ALA A 287 5 5 HELIX 14 14 PHE A 297 PHE A 299 5 3 HELIX 15 15 GLY A 307 GLY A 326 1 20 HELIX 16 16 THR A 331 TYR A 335 5 5 HELIX 17 17 ALA B 45 GLY B 56 1 12 HELIX 18 18 ASN B 65 GLY B 71 5 7 HELIX 19 19 ARG B 79 SER B 90 1 12 HELIX 20 20 MET B 102 CYS B 106 5 5 HELIX 21 21 THR B 113 GLY B 122 1 10 HELIX 22 22 ASP B 131 LEU B 150 1 20 HELIX 23 23 THR B 152 TYR B 156 5 5 HELIX 24 24 SER B 206 GLN B 222 1 17 HELIX 25 25 MET B 242 LEU B 247 5 6 HELIX 26 26 GLU B 249 LEU B 261 1 13 HELIX 27 27 CYS B 264 ILE B 269 1 6 HELIX 28 28 PRO B 271 LYS B 275 5 5 HELIX 29 29 THR B 283 ALA B 287 5 5 HELIX 30 30 PHE B 297 PHE B 299 5 3 HELIX 31 31 GLY B 307 ALA B 325 1 19 HELIX 32 32 THR B 331 TYR B 335 5 5 HELIX 33 33 THR B 420 GLN B 424 5 5 SHEET 1 A 5 ILE A 93 ASN A 96 0 SHEET 2 A 5 THR A 61 PHE A 64 1 N PHE A 62 O GLY A 95 SHEET 3 A 5 GLY A 32 ASP A 39 1 N PHE A 38 O TYR A 63 SHEET 4 A 5 LYS A 289 HIS A 295 1 O VAL A 290 N TYR A 35 SHEET 5 A 5 VAL A 231 ASP A 232 1 N VAL A 231 O LEU A 293 SHEET 1 B 4 ILE A 93 ASN A 96 0 SHEET 2 B 4 THR A 61 PHE A 64 1 N PHE A 62 O GLY A 95 SHEET 3 B 4 GLY A 32 ASP A 39 1 N PHE A 38 O TYR A 63 SHEET 4 B 4 TYR A 327 PHE A 329 1 O VAL A 328 N ILE A 34 SHEET 1 C 2 LEU A 164 ALA A 165 0 SHEET 2 C 2 GLN A 225 THR A 226 1 O GLN A 225 N ALA A 165 SHEET 1 D 2 TRP A 173 THR A 176 0 SHEET 2 D 2 PHE A 179 ALA A 181 -1 O ALA A 181 N TRP A 173 SHEET 1 E 2 ASP A 301 GLY A 302 0 SHEET 2 E 2 GLY A 305 MET A 306 -1 O GLY A 305 N GLY A 302 SHEET 1 F 2 THR A 344 TYR A 345 0 SHEET 2 F 2 HIS A 364 THR A 365 -1 O HIS A 364 N TYR A 345 SHEET 1 G 3 TYR A 350 TYR A 353 0 SHEET 2 G 3 VAL A 356 ALA A 360 -1 O VAL A 356 N TYR A 353 SHEET 3 G 3 TRP A 379 ASN A 381 -1 O THR A 380 N LYS A 359 SHEET 1 H 2 SER A 393 TYR A 394 0 SHEET 2 H 2 HIS A 413 VAL A 414 -1 O HIS A 413 N TYR A 394 SHEET 1 I 3 ILE A 399 TYR A 402 0 SHEET 2 I 3 LYS A 405 VAL A 409 -1 O LYS A 405 N TYR A 402 SHEET 3 I 3 PHE A 428 ALA A 430 -1 O THR A 429 N LEU A 408 SHEET 1 J 5 ILE B 93 ASN B 96 0 SHEET 2 J 5 THR B 61 PHE B 64 1 N PHE B 62 O GLY B 95 SHEET 3 J 5 GLY B 32 ASP B 39 1 N PHE B 38 O TYR B 63 SHEET 4 J 5 LYS B 289 HIS B 295 1 O VAL B 292 N TYR B 35 SHEET 5 J 5 VAL B 231 ASP B 232 1 N VAL B 231 O LEU B 293 SHEET 1 K 4 ILE B 93 ASN B 96 0 SHEET 2 K 4 THR B 61 PHE B 64 1 N PHE B 62 O GLY B 95 SHEET 3 K 4 GLY B 32 ASP B 39 1 N PHE B 38 O TYR B 63 SHEET 4 K 4 TYR B 327 PHE B 329 1 O VAL B 328 N ILE B 34 SHEET 1 L 2 LEU B 164 ALA B 165 0 SHEET 2 L 2 GLN B 225 THR B 226 1 O GLN B 225 N ALA B 165 SHEET 1 M 2 TRP B 173 THR B 176 0 SHEET 2 M 2 PHE B 179 ALA B 181 -1 O ALA B 181 N TRP B 173 SHEET 1 N 2 ASP B 301 GLY B 302 0 SHEET 2 N 2 GLY B 305 MET B 306 -1 O GLY B 305 N GLY B 302 SHEET 1 O 2 THR B 344 TYR B 345 0 SHEET 2 O 2 HIS B 364 THR B 365 -1 O HIS B 364 N TYR B 345 SHEET 1 P 3 TYR B 350 TYR B 353 0 SHEET 2 P 3 VAL B 356 ALA B 360 -1 O VAL B 356 N TYR B 353 SHEET 3 P 3 TRP B 379 ASN B 381 -1 O THR B 380 N LYS B 359 SHEET 1 Q 2 SER B 393 TYR B 394 0 SHEET 2 Q 2 HIS B 413 VAL B 414 -1 O HIS B 413 N TYR B 394 SHEET 1 R 3 ILE B 399 TYR B 402 0 SHEET 2 R 3 LYS B 405 VAL B 409 -1 O LYS B 405 N TYR B 402 SHEET 3 R 3 PHE B 428 ALA B 430 -1 O THR B 429 N LEU B 408 SSBOND 1 CYS A 106 CYS A 118 1555 1555 2.05 SSBOND 2 CYS A 185 CYS A 200 1555 1555 2.03 SSBOND 3 CYS A 264 CYS A 281 1555 1555 2.06 SSBOND 4 CYS B 106 CYS B 118 1555 1555 2.03 SSBOND 5 CYS B 185 CYS B 200 1555 1555 2.03 SSBOND 6 CYS B 264 CYS B 281 1555 1555 2.05 LINK OD1 ASP A 40 ZN ZN A 501 1555 1555 2.08 LINK NE2 HIS A 97 ZN ZN A 501 1555 1555 2.15 LINK NE2 HIS A 101 ZN ZN A 501 1555 1555 2.05 LINK O GLY A 223 CA CA A 502 1555 1555 2.26 LINK O GLY A 355 CA CA A 502 1555 1555 2.22 LINK ZN ZN A 501 OXT ACT A 503 1555 1555 1.98 LINK ZN ZN A 501 O ACT A 503 1555 1555 2.23 LINK ZN ZN A 501 O HOH A 724 1555 1555 2.34 LINK CA CA A 502 O HOH A 604 1555 1555 2.42 LINK CA CA A 502 O HOH A 605 1555 1555 2.43 LINK CA CA A 502 O HOH A 608 1555 1555 2.39 LINK CA CA A 502 O HOH A 653 1555 1555 2.23 LINK OD1 ASP B 40 ZN ZN B 501 1555 1555 2.04 LINK NE2 HIS B 97 ZN ZN B 501 1555 1555 2.16 LINK NE2 HIS B 101 ZN ZN B 501 1555 1555 2.03 LINK O GLY B 223 CA CA B 502 1555 1555 2.31 LINK O GLY B 355 CA CA B 502 1555 1555 2.23 LINK ZN ZN B 501 O ACT B 503 1555 1555 2.18 LINK ZN ZN B 501 OXT ACT B 503 1555 1555 2.20 LINK ZN ZN B 501 O HOH B 801 1555 1555 2.39 LINK CA CA B 502 O HOH B 603 1555 1555 2.39 LINK CA CA B 502 O HOH B 604 1555 1555 2.35 LINK CA CA B 502 O HOH B 606 1555 1555 2.25 LINK CA CA B 502 O HOH B 611 1555 1555 2.35 CISPEP 1 GLY A 41 PRO A 42 0 2.04 CISPEP 2 GLU A 270 PRO A 271 0 6.74 CISPEP 3 GLY B 41 PRO B 42 0 -3.20 CISPEP 4 GLU B 270 PRO B 271 0 4.82 SITE 1 AC1 5 ASP A 40 HIS A 97 HIS A 101 ACT A 503 SITE 2 AC1 5 HOH A 724 SITE 1 AC2 6 GLY A 223 GLY A 355 HOH A 604 HOH A 605 SITE 2 AC2 6 HOH A 608 HOH A 653 SITE 1 AC3 9 ASP A 39 ASP A 40 HIS A 97 HIS A 101 SITE 2 AC3 9 PRO A 168 TYR A 169 HIS A 295 ZN A 501 SITE 3 AC3 9 HOH A 724 SITE 1 AC4 8 GLU A 140 TYR A 162 GLN A 222 HOH A 619 SITE 2 AC4 8 HOH A 739 HOH A 744 GOL B 504 HOH B 825 SITE 1 AC5 5 ASP B 40 HIS B 97 HIS B 101 ACT B 503 SITE 2 AC5 5 HOH B 801 SITE 1 AC6 6 GLY B 223 GLY B 355 HOH B 603 HOH B 604 SITE 2 AC6 6 HOH B 606 HOH B 611 SITE 1 AC7 10 ASP B 39 ASP B 40 HIS B 97 HIS B 101 SITE 2 AC7 10 PRO B 168 TYR B 169 TRP B 229 HIS B 295 SITE 3 AC7 10 ZN B 501 HOH B 801 SITE 1 AC8 9 GOL A 504 HOH A 711 GLU B 140 TYR B 162 SITE 2 AC8 9 GLN B 222 TYR B 224 HOH B 630 HOH B 653 SITE 3 AC8 9 HOH B 905 CRYST1 61.900 112.540 69.360 90.00 94.05 90.00 P 1 21 1 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 0.016155 0.000000 0.001144 0.00000 SCALE2 0.000000 0.008886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014454 0.00000