HEADER HYDROLASE 20-SEP-19 6UE4 TITLE SHYA ENDOPEPTIDASE FROM VIBRIO CHOLERAE (CLOSED FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHYA ENDOPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE SEROTYPE O1 (STRAIN ATCC 39315 SOURCE 3 / EL TOR INABA N16961); SOURCE 4 ORGANISM_TAXID: 243277; SOURCE 5 STRAIN: ATCC 39315 / EL TOR INABA N16961; SOURCE 6 GENE: VC_A0079; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PLYSS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B-6XHIS-THROMBIN KEYWDS ENDOPEPTIDASE M23, LYTM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MAO,A.SULPIZIO REVDAT 3 11-OCT-23 6UE4 1 LINK REVDAT 2 10-JUN-20 6UE4 1 JRNL REVDAT 1 27-MAY-20 6UE4 0 JRNL AUTH J.H.SHIN,A.G.SULPIZIO,A.KELLEY,L.ALVAREZ,S.G.MURPHY,L.FAN, JRNL AUTH 2 F.CAVA,Y.MAO,M.A.SAPER,T.DORR JRNL TITL STRUCTURAL BASIS OF PEPTIDOGLYCAN ENDOPEPTIDASE REGULATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 11692 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32393643 JRNL DOI 10.1073/PNAS.2001661117 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 43887 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2297 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) : 2.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3223 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 156 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5632 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.76000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.314 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5752 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5410 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7757 ; 2.007 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12520 ; 1.394 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 702 ; 7.345 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;26.678 ;21.084 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1028 ;16.849 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;18.175 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 720 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6438 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1268 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 72 A 425 REMARK 3 ORIGIN FOR THE GROUP (A): 6.6541 -0.0980 17.5226 REMARK 3 T TENSOR REMARK 3 T11: 0.0082 T22: 0.0572 REMARK 3 T33: 0.0079 T12: -0.0007 REMARK 3 T13: -0.0007 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.1865 L22: 0.3958 REMARK 3 L33: 0.5046 L12: 0.0514 REMARK 3 L13: 0.1093 L23: 0.0093 REMARK 3 S TENSOR REMARK 3 S11: -0.0125 S12: -0.0263 S13: 0.0368 REMARK 3 S21: -0.0212 S22: 0.0069 S23: 0.0136 REMARK 3 S31: -0.0597 S32: 0.0069 S33: 0.0056 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 72 B 426 REMARK 3 ORIGIN FOR THE GROUP (A): 10.7211 -28.8262 18.1834 REMARK 3 T TENSOR REMARK 3 T11: 0.0115 T22: 0.0612 REMARK 3 T33: 0.0101 T12: 0.0136 REMARK 3 T13: 0.0087 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.4088 L22: 0.3886 REMARK 3 L33: 0.3569 L12: 0.1605 REMARK 3 L13: -0.0338 L23: 0.0654 REMARK 3 S TENSOR REMARK 3 S11: -0.0211 S12: 0.0117 S13: -0.0276 REMARK 3 S21: -0.0302 S22: 0.0120 S23: -0.0386 REMARK 3 S31: 0.0441 S32: 0.0247 S33: 0.0091 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6UE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000243973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97750 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46469 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2GU1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MALONIC ACID PH 6.0, 14% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 43.62600 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: 4520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 GLY A 32 REMARK 465 SER A 33 REMARK 465 HIS A 34 REMARK 465 MET A 35 REMARK 465 LEU A 36 REMARK 465 ASN A 37 REMARK 465 SER A 38 REMARK 465 PRO A 39 REMARK 465 THR A 40 REMARK 465 ARG A 41 REMARK 465 GLN A 42 REMARK 465 GLN A 43 REMARK 465 ARG A 44 REMARK 465 ILE A 45 REMARK 465 GLU A 46 REMARK 465 LEU A 47 REMARK 465 SER A 48 REMARK 465 LEU A 49 REMARK 465 PRO A 50 REMARK 465 GLU A 51 REMARK 465 SER A 52 REMARK 465 PRO A 53 REMARK 465 LEU A 54 REMARK 465 VAL A 55 REMARK 465 GLN A 56 REMARK 465 PHE A 57 REMARK 465 SER A 58 REMARK 465 SER A 59 REMARK 465 ALA A 60 REMARK 465 GLU A 61 REMARK 465 HIS A 62 REMARK 465 THR A 63 REMARK 465 VAL A 64 REMARK 465 GLU A 65 REMARK 465 VAL A 66 REMARK 465 VAL A 67 REMARK 465 LYS A 68 REMARK 465 VAL A 69 REMARK 465 GLY A 70 REMARK 465 HIS A 71 REMARK 465 MET A 426 REMARK 465 LEU A 427 REMARK 465 ALA A 428 REMARK 465 ALA A 429 REMARK 465 GLN A 430 REMARK 465 GLY B 32 REMARK 465 SER B 33 REMARK 465 HIS B 34 REMARK 465 MET B 35 REMARK 465 LEU B 36 REMARK 465 ASN B 37 REMARK 465 SER B 38 REMARK 465 PRO B 39 REMARK 465 THR B 40 REMARK 465 ARG B 41 REMARK 465 GLN B 42 REMARK 465 GLN B 43 REMARK 465 ARG B 44 REMARK 465 ILE B 45 REMARK 465 GLU B 46 REMARK 465 LEU B 47 REMARK 465 SER B 48 REMARK 465 LEU B 49 REMARK 465 PRO B 50 REMARK 465 GLU B 51 REMARK 465 SER B 52 REMARK 465 PRO B 53 REMARK 465 LEU B 54 REMARK 465 VAL B 55 REMARK 465 GLN B 56 REMARK 465 PHE B 57 REMARK 465 SER B 58 REMARK 465 SER B 59 REMARK 465 ALA B 60 REMARK 465 GLU B 61 REMARK 465 HIS B 62 REMARK 465 THR B 63 REMARK 465 VAL B 64 REMARK 465 GLU B 65 REMARK 465 VAL B 66 REMARK 465 VAL B 67 REMARK 465 LYS B 68 REMARK 465 VAL B 69 REMARK 465 GLY B 70 REMARK 465 HIS B 71 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 ASP B 127 REMARK 465 ASN B 128 REMARK 465 LEU B 427 REMARK 465 ALA B 428 REMARK 465 ALA B 429 REMARK 465 GLN B 430 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 127 42.04 -101.89 REMARK 500 ASP A 283 114.43 -160.53 REMARK 500 HIS A 335 65.39 -112.32 REMARK 500 ALA A 398 19.89 58.32 REMARK 500 HIS B 335 67.25 -114.31 REMARK 500 ASN B 368 28.69 -142.99 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 HIS A 297 NE2 REMARK 620 2 ASP A 301 OD1 108.5 REMARK 620 3 HIS A 378 ND1 109.7 104.8 REMARK 620 4 HOH A 632 O 123.7 103.9 104.7 REMARK 620 N 1 2 3 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 HIS B 297 NE2 REMARK 620 2 ASP B 301 OD1 106.0 REMARK 620 3 HIS B 378 ND1 112.5 105.1 REMARK 620 4 HOH B 655 O 128.2 102.9 100.0 REMARK 620 N 1 2 3 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 ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6U2A RELATED DB: PDB REMARK 900 OPEN CONFORMATION OF THIS ENTRY DBREF 6UE4 A 36 430 UNP Q9KN86 Q9KN86_VIBCH 36 430 DBREF 6UE4 B 36 430 UNP Q9KN86 Q9KN86_VIBCH 36 430 SEQADV 6UE4 GLY A 32 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 SER A 33 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 HIS A 34 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 MET A 35 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 GLY B 32 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 SER B 33 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 HIS B 34 UNP Q9KN86 EXPRESSION TAG SEQADV 6UE4 MET B 35 UNP Q9KN86 EXPRESSION TAG SEQRES 1 A 399 GLY SER HIS MET LEU ASN SER PRO THR ARG GLN GLN ARG SEQRES 2 A 399 ILE GLU LEU SER LEU PRO GLU SER PRO LEU VAL GLN PHE SEQRES 3 A 399 SER SER ALA GLU HIS THR VAL GLU VAL VAL LYS VAL GLY SEQRES 4 A 399 HIS PRO ASP TYR GLU TYR GLU ILE LYS PRO GLY ASP ASN SEQRES 5 A 399 LEU SER THR ILE PHE ASN GLN LEU GLY PHE ALA TYR THR SEQRES 6 A 399 GLU LEU MET LYS VAL MET GLU THR ASP LEU ASN TYR LEU SEQRES 7 A 399 ALA LEU ASP THR LEU ARG PRO GLY ASN VAL LEU ARG PHE SEQRES 8 A 399 TRP LYS GLY SER ASP ASN THR LEU ALA LYS MET GLU LEU SEQRES 9 A 399 GLU PHE SER LEU VAL ASP ARG ALA VAL TYR THR ARG LEU SEQRES 10 A 399 ASN ASP GLY SER TYR GLU PHE GLU GLU ARG LYS ILE PRO SEQRES 11 A 399 GLY THR TRP LYS VAL GLU PRO LEU ILE GLY GLU VAL ASP SEQRES 12 A 399 GLY SER PHE SER LEU SER ALA ASN ARG ALA GLY LEU GLY SEQRES 13 A 399 ALA ALA ASP VAL ASP GLN ILE VAL THR LEU LEU LYS ASP SEQRES 14 A 399 LYS ILE ASN PHE GLY ARG ASP LEU ARG ARG GLY ASP ARG SEQRES 15 A 399 PHE GLU VAL VAL LEU SER ARG GLN LEU VAL GLY GLU LYS SEQRES 16 A 399 LEU THR GLY ASN SER GLU ILE GLN ALA ILE LYS ILE PHE SEQRES 17 A 399 ASN ARG GLY LYS GLU ILE THR ALA TYR LEU HIS GLN ASP SEQRES 18 A 399 GLY GLN TYR TYR ASP LYS ASN GLY ASP SER LEU GLN ARG SEQRES 19 A 399 ALA PHE GLN ARG TYR PRO VAL ASP SER LYS TRP ARG ILE SEQRES 20 A 399 SER SER ASN PHE ASP PRO ARG ARG LEU HIS PRO VAL THR SEQRES 21 A 399 LYS ARG VAL ALA PRO HIS ASN GLY THR ASP PHE ALA MET SEQRES 22 A 399 PRO ILE GLY THR PRO VAL TYR THR SER GLY ASP GLY VAL SEQRES 23 A 399 VAL VAL MET THR ARG ASN HIS PRO TYR ALA GLY ASN TYR SEQRES 24 A 399 VAL VAL ILE GLN HIS GLY ASN THR TYR MET THR ARG TYR SEQRES 25 A 399 LEU HIS LEU SER LYS ILE LEU VAL LYS LYS GLY GLN LYS SEQRES 26 A 399 VAL SER ARG GLY GLN ARG ILE GLY LEU SER GLY ASN THR SEQRES 27 A 399 GLY ARG VAL THR GLY PRO HIS LEU HIS TYR GLU LEU ILE SEQRES 28 A 399 VAL ARG GLY ARG PRO VAL ASN ALA MET LYS ALA ASN ILE SEQRES 29 A 399 PRO MET ALA SER SER VAL PRO LYS LYS GLU MET ALA GLN SEQRES 30 A 399 PHE ILE ALA LYS ARG LYS GLU LEU ASP GLN MET LEU ALA SEQRES 31 A 399 ARG GLN GLU SER MET LEU ALA ALA GLN SEQRES 1 B 399 GLY SER HIS MET LEU ASN SER PRO THR ARG GLN GLN ARG SEQRES 2 B 399 ILE GLU LEU SER LEU PRO GLU SER PRO LEU VAL GLN PHE SEQRES 3 B 399 SER SER ALA GLU HIS THR VAL GLU VAL VAL LYS VAL GLY SEQRES 4 B 399 HIS PRO ASP TYR GLU TYR GLU ILE LYS PRO GLY ASP ASN SEQRES 5 B 399 LEU SER THR ILE PHE ASN GLN LEU GLY PHE ALA TYR THR SEQRES 6 B 399 GLU LEU MET LYS VAL MET GLU THR ASP LEU ASN TYR LEU SEQRES 7 B 399 ALA LEU ASP THR LEU ARG PRO GLY ASN VAL LEU ARG PHE SEQRES 8 B 399 TRP LYS GLY SER ASP ASN THR LEU ALA LYS MET GLU LEU SEQRES 9 B 399 GLU PHE SER LEU VAL ASP ARG ALA VAL TYR THR ARG LEU SEQRES 10 B 399 ASN ASP GLY SER TYR GLU PHE GLU GLU ARG LYS ILE PRO SEQRES 11 B 399 GLY THR TRP LYS VAL GLU PRO LEU ILE GLY GLU VAL ASP SEQRES 12 B 399 GLY SER PHE SER LEU SER ALA ASN ARG ALA GLY LEU GLY SEQRES 13 B 399 ALA ALA ASP VAL ASP GLN ILE VAL THR LEU LEU LYS ASP SEQRES 14 B 399 LYS ILE ASN PHE GLY ARG ASP LEU ARG ARG GLY ASP ARG SEQRES 15 B 399 PHE GLU VAL VAL LEU SER ARG GLN LEU VAL GLY GLU LYS SEQRES 16 B 399 LEU THR GLY ASN SER GLU ILE GLN ALA ILE LYS ILE PHE SEQRES 17 B 399 ASN ARG GLY LYS GLU ILE THR ALA TYR LEU HIS GLN ASP SEQRES 18 B 399 GLY GLN TYR TYR ASP LYS ASN GLY ASP SER LEU GLN ARG SEQRES 19 B 399 ALA PHE GLN ARG TYR PRO VAL ASP SER LYS TRP ARG ILE SEQRES 20 B 399 SER SER ASN PHE ASP PRO ARG ARG LEU HIS PRO VAL THR SEQRES 21 B 399 LYS ARG VAL ALA PRO HIS ASN GLY THR ASP PHE ALA MET SEQRES 22 B 399 PRO ILE GLY THR PRO VAL TYR THR SER GLY ASP GLY VAL SEQRES 23 B 399 VAL VAL MET THR ARG ASN HIS PRO TYR ALA GLY ASN TYR SEQRES 24 B 399 VAL VAL ILE GLN HIS GLY ASN THR TYR MET THR ARG TYR SEQRES 25 B 399 LEU HIS LEU SER LYS ILE LEU VAL LYS LYS GLY GLN LYS SEQRES 26 B 399 VAL SER ARG GLY GLN ARG ILE GLY LEU SER GLY ASN THR SEQRES 27 B 399 GLY ARG VAL THR GLY PRO HIS LEU HIS TYR GLU LEU ILE SEQRES 28 B 399 VAL ARG GLY ARG PRO VAL ASN ALA MET LYS ALA ASN ILE SEQRES 29 B 399 PRO MET ALA SER SER VAL PRO LYS LYS GLU MET ALA GLN SEQRES 30 B 399 PHE ILE ALA LYS ARG LYS GLU LEU ASP GLN MET LEU ALA SEQRES 31 B 399 ARG GLN GLU SER MET LEU ALA ALA GLN HET ZN A 501 1 HET ZN B 501 1 HET GOL B 502 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *227(H2 O) HELIX 1 AA1 ASN A 83 GLY A 92 1 10 HELIX 2 AA2 ALA A 94 LEU A 106 1 13 HELIX 3 AA3 ALA A 110 LEU A 114 5 5 HELIX 4 AA4 SER A 176 ALA A 184 1 9 HELIX 5 AA5 GLY A 187 LYS A 199 1 13 HELIX 6 AA6 ASN A 203 LEU A 208 1 6 HELIX 7 AA7 PRO A 402 LYS A 404 5 3 HELIX 8 AA8 GLU A 405 SER A 425 1 21 HELIX 9 AA9 ASN B 83 GLY B 92 1 10 HELIX 10 AB1 ALA B 94 LEU B 106 1 13 HELIX 11 AB2 ALA B 110 LEU B 114 5 5 HELIX 12 AB3 SER B 176 GLY B 185 1 10 HELIX 13 AB4 GLY B 187 LYS B 199 1 13 HELIX 14 AB5 PRO B 402 LYS B 404 5 3 HELIX 15 AB6 GLU B 405 MET B 426 1 22 SHEET 1 AA1 5 TYR A 74 GLU A 77 0 SHEET 2 AA1 5 VAL A 119 LYS A 124 -1 O LEU A 120 N TYR A 76 SHEET 3 AA1 5 LEU A 130 SER A 138 -1 O GLU A 136 N VAL A 119 SHEET 4 AA1 5 ASP A 141 ARG A 147 -1 O ALA A 143 N LEU A 135 SHEET 5 AA1 5 TYR A 153 LYS A 159 -1 O ARG A 158 N ARG A 142 SHEET 1 AA2 7 TYR A 255 TYR A 256 0 SHEET 2 AA2 7 LYS A 243 LEU A 249 -1 N TYR A 248 O TYR A 256 SHEET 3 AA2 7 LYS A 226 ASN A 240 -1 N ILE A 238 O ILE A 245 SHEET 4 AA2 7 ARG A 213 VAL A 223 -1 N VAL A 217 O GLN A 234 SHEET 5 AA2 7 THR A 163 GLU A 172 -1 N LEU A 169 O VAL A 216 SHEET 6 AA2 7 ARG B 293 HIS B 297 -1 O VAL B 294 N TRP A 164 SHEET 7 AA2 7 ASP B 283 HIS B 288 -1 N ASP B 283 O HIS B 297 SHEET 1 AA3 7 ILE A 278 SER A 280 0 SHEET 2 AA3 7 THR A 300 ALA A 303 -1 O ASP A 301 N SER A 280 SHEET 3 AA3 7 HIS A 376 VAL A 383 -1 O TYR A 379 N THR A 300 SHEET 4 AA3 7 TYR A 339 LEU A 346 -1 N MET A 340 O ILE A 382 SHEET 5 AA3 7 GLY A 328 HIS A 335 -1 N HIS A 335 O TYR A 339 SHEET 6 AA3 7 GLY A 316 HIS A 324 -1 N HIS A 324 O GLY A 328 SHEET 7 AA3 7 LYS A 356 VAL A 357 -1 O VAL A 357 N GLY A 316 SHEET 1 AA4 4 ILE A 278 SER A 280 0 SHEET 2 AA4 4 THR A 300 ALA A 303 -1 O ASP A 301 N SER A 280 SHEET 3 AA4 4 HIS A 376 VAL A 383 -1 O TYR A 379 N THR A 300 SHEET 4 AA4 4 ARG A 386 VAL A 388 -1 O ARG A 386 N VAL A 383 SHEET 1 AA5 7 ASP A 283 HIS A 288 0 SHEET 2 AA5 7 ARG A 293 HIS A 297 -1 O ARG A 293 N HIS A 288 SHEET 3 AA5 7 THR B 163 GLU B 172 -1 O TRP B 164 N VAL A 294 SHEET 4 AA5 7 ARG B 213 VAL B 223 -1 O VAL B 216 N LEU B 169 SHEET 5 AA5 7 LYS B 226 ASN B 240 -1 O LYS B 237 N GLU B 215 SHEET 6 AA5 7 LYS B 243 LEU B 249 -1 O ILE B 245 N ILE B 238 SHEET 7 AA5 7 TYR B 255 TYR B 256 -1 O TYR B 256 N TYR B 248 SHEET 1 AA6 3 PRO A 309 TYR A 311 0 SHEET 2 AA6 3 ARG A 362 LEU A 365 -1 O GLY A 364 N VAL A 310 SHEET 3 AA6 3 LYS A 348 ILE A 349 -1 N LYS A 348 O LEU A 365 SHEET 1 AA7 5 TYR B 74 GLU B 77 0 SHEET 2 AA7 5 VAL B 119 TRP B 123 -1 O LEU B 120 N TYR B 76 SHEET 3 AA7 5 LYS B 132 GLU B 136 -1 O GLU B 136 N VAL B 119 SHEET 4 AA7 5 ASP B 141 ARG B 147 -1 O ALA B 143 N LEU B 135 SHEET 5 AA7 5 TYR B 153 LYS B 159 -1 O GLU B 154 N THR B 146 SHEET 1 AA8 7 ILE B 278 SER B 280 0 SHEET 2 AA8 7 THR B 300 ALA B 303 -1 O ASP B 301 N SER B 280 SHEET 3 AA8 7 HIS B 376 VAL B 383 -1 O TYR B 379 N THR B 300 SHEET 4 AA8 7 TYR B 339 LEU B 346 -1 N MET B 340 O ILE B 382 SHEET 5 AA8 7 GLY B 328 HIS B 335 -1 N ILE B 333 O THR B 341 SHEET 6 AA8 7 GLY B 316 HIS B 324 -1 N VAL B 317 O GLN B 334 SHEET 7 AA8 7 LYS B 356 VAL B 357 -1 O VAL B 357 N GLY B 316 SHEET 1 AA9 4 ILE B 278 SER B 280 0 SHEET 2 AA9 4 THR B 300 ALA B 303 -1 O ASP B 301 N SER B 280 SHEET 3 AA9 4 HIS B 376 VAL B 383 -1 O TYR B 379 N THR B 300 SHEET 4 AA9 4 ARG B 386 VAL B 388 -1 O VAL B 388 N LEU B 381 SHEET 1 AB1 3 PRO B 309 TYR B 311 0 SHEET 2 AB1 3 ARG B 362 LEU B 365 -1 O ILE B 363 N VAL B 310 SHEET 3 AB1 3 LYS B 348 ILE B 349 -1 N LYS B 348 O LEU B 365 LINK NE2 HIS A 297 ZN ZN A 501 1555 1555 1.98 LINK OD1 ASP A 301 ZN ZN A 501 1555 1555 1.99 LINK ND1 HIS A 378 ZN ZN A 501 1555 1555 1.93 LINK ZN ZN A 501 O HOH A 632 1555 1555 2.20 LINK NE2 HIS B 297 ZN ZN B 501 1555 1555 2.10 LINK OD1 ASP B 301 ZN ZN B 501 1555 1555 2.02 LINK ND1 HIS B 378 ZN ZN B 501 1555 1555 1.97 LINK ZN ZN B 501 O HOH B 655 1555 1555 2.12 SITE 1 AC1 4 HIS A 297 ASP A 301 HIS A 378 HOH A 632 SITE 1 AC2 4 HIS B 297 ASP B 301 HIS B 378 HOH B 655 SITE 1 AC3 3 GLY B 117 ASN B 118 GLU B 136 CRYST1 61.115 87.252 74.973 90.00 100.37 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 0.016363 0.000000 0.002995 0.00000 SCALE2 0.000000 0.011461 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013560 0.00000