HEADER HYDROLASE 23-AUG-19 6KSG TITLE VIBRIO CHOLERAE METHIONINE AMINOPEPTIDASE IN HOLO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METAP,PEPTIDASE M; COMPND 5 EC: 3.4.11.18; COMPND 6 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: MAP, VC_2261; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.PILLALAMARRI,A.ADDLAGATTA REVDAT 4 22-NOV-23 6KSG 1 REMARK REVDAT 3 27-JAN-21 6KSG 1 REMARK REVDAT 2 02-DEC-20 6KSG 1 JRNL REVDAT 1 26-AUG-20 6KSG 0 JRNL AUTH V.PILLALAMARRI,C.G.REDDY,S.C.BALA,A.JANGAM,V.V.KUTTY, JRNL AUTH 2 A.ADDLAGATTA JRNL TITL METHIONINE AMINOPEPTIDASES WITH SHORT SEQUENCE INSERTS JRNL TITL 2 WITHIN THE CATALYTIC DOMAIN ARE DIFFERENTIALLY INHIBITED: JRNL TITL 3 STRUCTURAL AND BIOCHEMICAL STUDIES OF THREE PROTEINS FROM JRNL TITL 4 VIBRIO SPP. JRNL REF EUR.J.MED.CHEM. V. 209 12883 2020 JRNL REFN ISSN 0223-5234 JRNL PMID 33035924 JRNL DOI 10.1016/J.EJMECH.2020.112883 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 47497 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2495 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3452 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 167 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4378 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.61000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : 0.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.566 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4548 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4254 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6156 ; 1.542 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9918 ; 1.380 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 572 ; 6.955 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;35.507 ;23.276 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 816 ;14.345 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.104 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 618 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5064 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 880 ; 0.003 ; 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 : 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: MOLECULAR REPLCEMENT REMARK 4 REMARK 4 6KSG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9536 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.79500 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: MOLREP REMARK 200 STARTING MODEL: 6K26 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 24.91750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ALA A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 MET A 1 REMARK 465 MET B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 LEU B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 ALA B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 MET B 1 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 ASN A 74 -109.45 58.75 REMARK 500 ASN A 174 59.98 -149.38 REMARK 500 GLU A 220 61.48 -155.31 REMARK 500 SER A 237 -6.14 71.46 REMARK 500 ASN B 74 -114.13 57.78 REMARK 500 PHE B 89 78.90 -69.41 REMARK 500 ALA B 96 -16.10 -142.81 REMARK 500 GLU B 220 60.37 -156.92 REMARK 500 SER B 237 -13.05 76.36 REMARK 500 SER B 272 51.09 -95.39 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 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 74 O REMARK 620 2 ILE A 76 O 98.3 REMARK 620 3 SER A 248 O 93.2 130.9 REMARK 620 4 HOH A 429 O 128.2 113.9 94.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 CG REMARK 620 2 ASP A 107 OD1 29.8 REMARK 620 3 ASP A 107 OD2 28.5 58.3 REMARK 620 4 ASP A 118 OD1 125.1 97.6 149.4 REMARK 620 5 GLU A 252 OE1 107.0 101.3 107.6 94.7 REMARK 620 6 HOH A 474 O 111.9 141.2 83.9 114.1 97.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 118 OD2 REMARK 620 2 HIS A 188 NE2 96.6 REMARK 620 3 GLU A 220 OE2 146.1 82.4 REMARK 620 4 GLU A 252 OE2 75.5 127.6 78.5 REMARK 620 5 HOH A 474 O 94.7 133.4 110.6 99.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 74 O REMARK 620 2 ILE B 76 O 96.3 REMARK 620 3 SER B 248 O 91.1 131.5 REMARK 620 4 HOH B 435 O 126.8 116.4 95.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 107 OD1 REMARK 620 2 ASP B 118 CG 125.8 REMARK 620 3 ASP B 118 OD1 100.8 25.1 REMARK 620 4 GLU B 252 OE1 99.1 80.9 86.1 REMARK 620 5 HOH B 427 O 117.5 116.7 141.5 91.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 118 OD2 REMARK 620 2 GLU B 220 OE2 123.7 REMARK 620 3 HOH B 427 O 102.7 99.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6K26 RELATED DB: PDB DBREF 6KSG A 1 280 UNP Q9KPV1 Q9KPV1_VIBCH 1 280 DBREF 6KSG B 1 280 UNP Q9KPV1 Q9KPV1_VIBCH 1 280 SEQADV 6KSG MET A -20 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG GLY A -19 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER A -18 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER A -17 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -16 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -15 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -14 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -13 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -12 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -11 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER A -10 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER A -9 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG GLY A -8 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG LEU A -7 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG VAL A -6 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG PRO A -5 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG ALA A -4 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG GLY A -3 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER A -2 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS A -1 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG MET A 0 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG MET B -20 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG GLY B -19 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER B -18 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER B -17 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -16 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -15 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -14 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -13 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -12 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -11 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER B -10 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER B -9 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG GLY B -8 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG LEU B -7 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG VAL B -6 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG PRO B -5 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG ALA B -4 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG GLY B -3 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG SER B -2 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG HIS B -1 UNP Q9KPV1 EXPRESSION TAG SEQADV 6KSG MET B 0 UNP Q9KPV1 EXPRESSION TAG SEQRES 1 A 301 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 301 LEU VAL PRO ALA GLY SER HIS MET MET SER ILE LYS ILE SEQRES 3 A 301 LYS ASN ALA VAL GLU ILE GLU LYS MET ARG VAL ALA GLY SEQRES 4 A 301 ARG LEU ALA ALA GLU VAL LEU GLU MET ILE GLU PRO HIS SEQRES 5 A 301 VAL LYS ALA GLY VAL THR THR GLU GLU LEU ASP GLN ILE SEQRES 6 A 301 CYS HIS LYS TYR ILE THR GLU VAL GLN GLY ALA ILE PRO SEQRES 7 A 301 ALA PRO LEU ASN TYR HIS GLY PHE PRO LYS SER ILE CYS SEQRES 8 A 301 THR SER ILE ASN HIS ILE VAL CYS HIS GLY ILE PRO ALA SEQRES 9 A 301 SER GLU ASP THR TYR PHE GLY GLN ILE GLN ARG PRO ALA SEQRES 10 A 301 VAL LEU ARG ASP GLY ASP ILE LEU ASN ILE ASP ILE THR SEQRES 11 A 301 VAL ILE LYS ASP GLY TYR HIS GLY ASP THR SER LYS MET SEQRES 12 A 301 PHE LEU ILE GLY ASP VAL SER ILE GLU ASP LYS ARG LEU SEQRES 13 A 301 CYS HIS VAL ALA GLN GLU CYS LEU TYR LEU ALA LEU LYS SEQRES 14 A 301 GLN VAL LYS PRO GLY VAL GLN LEU GLY GLU ILE GLY THR SEQRES 15 A 301 THR ILE GLU LYS HIS ILE LYS THR ASN ASN LYS ASN ASN SEQRES 16 A 301 PRO ARG PHE LYS PHE SER ILE VAL ARG ASP TYR CYS GLY SEQRES 17 A 301 HIS GLY ILE GLY ALA GLU PHE HIS GLU GLU PRO GLN VAL SEQRES 18 A 301 VAL HIS TYR LYS ASN SER ASP ARG THR VAL LEU ARG GLU SEQRES 19 A 301 GLY MET ILE PHE THR ILE GLU PRO MET ILE ASN ALA GLY SEQRES 20 A 301 LYS PHE GLY CYS ARG LEU ASP ASP GLU ASP SER TRP THR SEQRES 21 A 301 VAL TYR THR ALA ASP GLY LYS LYS SER ALA GLN TRP GLU SEQRES 22 A 301 HIS THR ILE LEU VAL THR ALA THR GLY CYS GLU ILE LEU SEQRES 23 A 301 THR LEU ARG SER GLU GLU SER LEU PRO ARG ILE LEU ASN SEQRES 24 A 301 ASN ALA SEQRES 1 B 301 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 301 LEU VAL PRO ALA GLY SER HIS MET MET SER ILE LYS ILE SEQRES 3 B 301 LYS ASN ALA VAL GLU ILE GLU LYS MET ARG VAL ALA GLY SEQRES 4 B 301 ARG LEU ALA ALA GLU VAL LEU GLU MET ILE GLU PRO HIS SEQRES 5 B 301 VAL LYS ALA GLY VAL THR THR GLU GLU LEU ASP GLN ILE SEQRES 6 B 301 CYS HIS LYS TYR ILE THR GLU VAL GLN GLY ALA ILE PRO SEQRES 7 B 301 ALA PRO LEU ASN TYR HIS GLY PHE PRO LYS SER ILE CYS SEQRES 8 B 301 THR SER ILE ASN HIS ILE VAL CYS HIS GLY ILE PRO ALA SEQRES 9 B 301 SER GLU ASP THR TYR PHE GLY GLN ILE GLN ARG PRO ALA SEQRES 10 B 301 VAL LEU ARG ASP GLY ASP ILE LEU ASN ILE ASP ILE THR SEQRES 11 B 301 VAL ILE LYS ASP GLY TYR HIS GLY ASP THR SER LYS MET SEQRES 12 B 301 PHE LEU ILE GLY ASP VAL SER ILE GLU ASP LYS ARG LEU SEQRES 13 B 301 CYS HIS VAL ALA GLN GLU CYS LEU TYR LEU ALA LEU LYS SEQRES 14 B 301 GLN VAL LYS PRO GLY VAL GLN LEU GLY GLU ILE GLY THR SEQRES 15 B 301 THR ILE GLU LYS HIS ILE LYS THR ASN ASN LYS ASN ASN SEQRES 16 B 301 PRO ARG PHE LYS PHE SER ILE VAL ARG ASP TYR CYS GLY SEQRES 17 B 301 HIS GLY ILE GLY ALA GLU PHE HIS GLU GLU PRO GLN VAL SEQRES 18 B 301 VAL HIS TYR LYS ASN SER ASP ARG THR VAL LEU ARG GLU SEQRES 19 B 301 GLY MET ILE PHE THR ILE GLU PRO MET ILE ASN ALA GLY SEQRES 20 B 301 LYS PHE GLY CYS ARG LEU ASP ASP GLU ASP SER TRP THR SEQRES 21 B 301 VAL TYR THR ALA ASP GLY LYS LYS SER ALA GLN TRP GLU SEQRES 22 B 301 HIS THR ILE LEU VAL THR ALA THR GLY CYS GLU ILE LEU SEQRES 23 B 301 THR LEU ARG SER GLU GLU SER LEU PRO ARG ILE LEU ASN SEQRES 24 B 301 ASN ALA HET NI A 301 1 HET NI A 302 1 HET NA A 303 1 HET GOL A 304 6 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HET NI B 301 1 HET NI B 302 1 HET NA B 303 1 HET GOL B 304 6 HET GOL B 305 6 HETNAM NI NICKEL (II) ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NI 4(NI 2+) FORMUL 5 NA 2(NA 1+) FORMUL 6 GOL 6(C3 H8 O3) FORMUL 15 HOH *209(H2 O) HELIX 1 AA1 ASN A 7 GLU A 29 1 23 HELIX 2 AA2 PRO A 30 VAL A 32 5 3 HELIX 3 AA3 THR A 37 VAL A 52 1 16 HELIX 4 AA4 ALA A 58 HIS A 63 1 6 HELIX 5 AA5 SER A 129 LYS A 148 1 20 HELIX 6 AA6 LEU A 156 ASN A 174 1 19 HELIX 7 AA7 ASN B 7 GLU B 29 1 23 HELIX 8 AA8 PRO B 30 VAL B 32 5 3 HELIX 9 AA9 THR B 37 VAL B 52 1 16 HELIX 10 AB1 ALA B 58 HIS B 63 1 6 HELIX 11 AB2 SER B 129 LYS B 148 1 20 HELIX 12 AB3 GLY B 157 ASN B 174 1 18 SHEET 1 AA1 3 ILE A 56 PRO A 57 0 SHEET 2 AA1 3 ILE A 103 LYS A 112 -1 O ILE A 111 N ILE A 56 SHEET 3 AA1 3 CYS A 70 ILE A 73 -1 N SER A 72 O ASN A 105 SHEET 1 AA2 3 ILE A 56 PRO A 57 0 SHEET 2 AA2 3 ILE A 103 LYS A 112 -1 O ILE A 111 N ILE A 56 SHEET 3 AA2 3 TYR A 115 LEU A 124 -1 O THR A 119 N ILE A 108 SHEET 1 AA3 3 ILE A 76 CYS A 78 0 SHEET 2 AA3 3 VAL A 240 THR A 242 -1 O VAL A 240 N VAL A 77 SHEET 3 AA3 3 CYS A 230 LEU A 232 -1 N ARG A 231 O TYR A 241 SHEET 1 AA4 2 THR A 87 PHE A 89 0 SHEET 2 AA4 2 ILE A 92 ARG A 94 -1 O ILE A 92 N PHE A 89 SHEET 1 AA5 3 SER A 180 ILE A 181 0 SHEET 2 AA5 3 MET A 222 ASN A 224 -1 O ASN A 224 N SER A 180 SHEET 3 AA5 3 SER A 248 GLN A 250 -1 O ALA A 249 N ILE A 223 SHEET 1 AA6 2 GLY A 187 GLY A 189 0 SHEET 2 AA6 2 GLU A 196 VAL A 200 -1 O VAL A 200 N GLY A 187 SHEET 1 AA7 4 ILE A 216 ILE A 219 0 SHEET 2 AA7 4 HIS A 253 VAL A 257 -1 O ILE A 255 N PHE A 217 SHEET 3 AA7 4 GLY A 261 ILE A 264 -1 O GLU A 263 N LEU A 256 SHEET 4 AA7 4 ILE A 276 ASN A 278 -1 O LEU A 277 N CYS A 262 SHEET 1 AA8 3 ILE B 56 PRO B 57 0 SHEET 2 AA8 3 ILE B 103 LYS B 112 -1 O ILE B 111 N ILE B 56 SHEET 3 AA8 3 CYS B 70 ILE B 73 -1 N SER B 72 O ASN B 105 SHEET 1 AA9 3 ILE B 56 PRO B 57 0 SHEET 2 AA9 3 ILE B 103 LYS B 112 -1 O ILE B 111 N ILE B 56 SHEET 3 AA9 3 TYR B 115 LEU B 124 -1 O THR B 119 N ILE B 108 SHEET 1 AB1 3 ILE B 76 CYS B 78 0 SHEET 2 AB1 3 VAL B 240 THR B 242 -1 O VAL B 240 N VAL B 77 SHEET 3 AB1 3 CYS B 230 LEU B 232 -1 N ARG B 231 O TYR B 241 SHEET 1 AB2 2 THR B 87 PHE B 89 0 SHEET 2 AB2 2 ILE B 92 ARG B 94 -1 O ARG B 94 N THR B 87 SHEET 1 AB3 3 SER B 180 ILE B 181 0 SHEET 2 AB3 3 MET B 222 ASN B 224 -1 O ASN B 224 N SER B 180 SHEET 3 AB3 3 SER B 248 GLN B 250 -1 O ALA B 249 N ILE B 223 SHEET 1 AB4 2 GLY B 187 GLY B 189 0 SHEET 2 AB4 2 GLU B 196 VAL B 200 -1 O VAL B 200 N GLY B 187 SHEET 1 AB5 4 ILE B 216 ILE B 219 0 SHEET 2 AB5 4 HIS B 253 VAL B 257 -1 O ILE B 255 N PHE B 217 SHEET 3 AB5 4 GLY B 261 ILE B 264 -1 O GLU B 263 N LEU B 256 SHEET 4 AB5 4 ILE B 276 ASN B 278 -1 O LEU B 277 N CYS B 262 LINK O ASN A 74 NA NA A 303 1555 1555 2.37 LINK O ILE A 76 NA NA A 303 1555 1555 2.39 LINK CG ASP A 107 NI NI A 301 1555 1555 2.53 LINK OD1 ASP A 107 NI NI A 301 1555 1555 2.10 LINK OD2 ASP A 107 NI NI A 301 1555 1555 2.35 LINK OD1 ASP A 118 NI NI A 301 1555 1555 2.33 LINK OD2 ASP A 118 NI NI A 302 1555 1555 2.08 LINK NE2 HIS A 188 NI NI A 302 1555 1555 2.75 LINK OE2 GLU A 220 NI NI A 302 1555 1555 2.55 LINK O SER A 248 NA NA A 303 1555 1555 2.14 LINK OE1 GLU A 252 NI NI A 301 1555 1555 2.21 LINK OE2 GLU A 252 NI NI A 302 1555 1555 2.28 LINK NI NI A 301 O HOH A 474 1555 1555 1.97 LINK NI NI A 302 O HOH A 474 1555 1555 2.51 LINK NA NA A 303 O HOH A 429 1555 1555 2.09 LINK O ASN B 74 NA NA B 303 1555 1555 2.44 LINK O ILE B 76 NA NA B 303 1555 1555 2.31 LINK OD1 ASP B 107 NI NI B 301 1555 1555 2.22 LINK CG ASP B 118 NI NI B 301 1555 1555 2.80 LINK OD1 ASP B 118 NI NI B 301 1555 1555 2.17 LINK OD2 ASP B 118 NI NI B 302 1555 1555 2.37 LINK OE2 GLU B 220 NI NI B 302 1555 1555 2.72 LINK O SER B 248 NA NA B 303 1555 1555 2.33 LINK OE1 GLU B 252 NI NI B 301 1555 1555 2.23 LINK NI NI B 301 O HOH B 427 1555 1555 2.30 LINK NI NI B 302 O HOH B 427 1555 1555 2.35 LINK NA NA B 303 O HOH B 435 1555 1555 2.15 CISPEP 1 GLU A 197 PRO A 198 0 -2.45 CISPEP 2 GLU B 197 PRO B 198 0 0.20 SITE 1 AC1 5 ASP A 107 ASP A 118 GLU A 252 NI A 302 SITE 2 AC1 5 HOH A 474 SITE 1 AC2 6 ASP A 118 HIS A 188 GLU A 220 GLU A 252 SITE 2 AC2 6 NI A 301 HOH A 474 SITE 1 AC3 4 ASN A 74 ILE A 76 SER A 248 HOH A 429 SITE 1 AC4 5 GLU A 85 ASP A 86 THR A 209 VAL A 210 SITE 2 AC4 5 ARG A 212 SITE 1 AC5 5 GLU A 29 VAL A 32 PHE A 123 LEU A 124 SITE 2 AC5 5 HOH A 473 SITE 1 AC6 7 GLY A 54 ILE A 56 ILE A 111 LYS A 112 SITE 2 AC6 7 ASP A 113 GLY A 114 ASN A 173 SITE 1 AC7 6 GLU A 164 SER A 180 ILE A 181 TYR A 203 SITE 2 AC7 6 HOH A 404 HOH A 454 SITE 1 AC8 5 ASP B 107 ASP B 118 GLU B 252 NI B 302 SITE 2 AC8 5 HOH B 427 SITE 1 AC9 7 ASP B 118 HIS B 188 PHE B 194 GLU B 220 SITE 2 AC9 7 GLU B 252 NI B 301 HOH B 427 SITE 1 AD1 4 ASN B 74 ILE B 76 SER B 248 HOH B 435 SITE 1 AD2 6 GLU B 85 ASP B 86 VAL B 97 THR B 209 SITE 2 AD2 6 VAL B 210 ARG B 212 SITE 1 AD3 4 GLU B 164 SER B 180 ILE B 181 ARG B 183 CRYST1 49.508 49.835 131.221 90.00 97.28 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 0.020199 0.000000 0.002580 0.00000 SCALE2 0.000000 0.020066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007683 0.00000