HEADER TOXIN/ANTITOXIN 19-SEP-18 6IFC TITLE CRYSTAL STRUCTURE OF VAPBC FROM SALMONELLA TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(FMET)-SPECIFIC ENDONUCLEASE VAPC; COMPND 3 CHAIN: A, C, E, G; COMPND 4 SYNONYM: RNASE VAPC,TOXIN VAPC; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ANTITOXIN VAPB; COMPND 9 CHAIN: B, F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ANTITOXIN VAPB; COMPND 13 CHAIN: D, H; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / SOURCE 3 ATCC 700720); SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: VAPC, STM3033; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / SOURCE 11 ATCC 700720); SOURCE 12 ORGANISM_TAXID: 99287; SOURCE 13 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 14 GENE: VAPB, STM3034; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / SOURCE 19 ATCC 700720); SOURCE 20 ORGANISM_TAXID: 99287; SOURCE 21 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 22 GENE: VAPB, STM3034; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN-ANTITOXIN, TOXIN-ANTITOXIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.W.PARK,B.J.LEE REVDAT 3 22-NOV-23 6IFC 1 LINK REVDAT 2 26-FEB-20 6IFC 1 JRNL REVDAT 1 29-JAN-20 6IFC 0 JRNL AUTH D.PARK,H.J.YOON,K.Y.LEE,S.J.PARK,S.H.CHEON,H.H.LEE,S.J.LEE, JRNL AUTH 2 B.J.LEE JRNL TITL CRYSTAL STRUCTURE OF PROTEOLYZED VAPBC AND DNA-BOUND VAPBC JRNL TITL 2 FROM SALMONELLA ENTERICA TYPHIMURIUM LT2 AND VAPC AS A JRNL TITL 3 PUTATIVE CA2+-DEPENDENT RIBONUCLEASE. JRNL REF FASEB J. V. 34 3051 2020 JRNL REFN ESSN 1530-6860 JRNL PMID 31908032 JRNL DOI 10.1096/FJ.201901989R REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 36229 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1905 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) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2581 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 141 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4976 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.53000 REMARK 3 B22 (A**2) : -0.98000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.211 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.751 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5070 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4824 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6848 ; 1.590 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11082 ; 0.837 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 620 ; 6.165 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 242 ;35.912 ;23.388 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 892 ;15.613 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;19.388 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 760 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5698 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1182 ; 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): 2504 ; 3.002 ; 3.380 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2503 ; 2.994 ; 3.379 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3116 ; 4.257 ; 5.042 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3117 ; 4.256 ; 5.044 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2566 ; 3.919 ; 3.860 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2567 ; 3.918 ; 3.861 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3733 ; 6.022 ; 5.616 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6018 ; 8.057 ;27.512 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5976 ; 8.056 ;27.451 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 : 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 REMARK 4 REMARK 4 6IFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300008902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NONIUS KAPPA CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38222 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 57.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MOLREP REMARK 200 STARTING MODEL: 3TND REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M CAPS/ REMARK 280 SODIUM HYDROXIDE PH 10.5, 2M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 57.47100 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 ILE D 39 REMARK 465 ILE H 39 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 OE2 GLU C 68 OE1 GLN E 75 1554 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 127 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES 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 MET B 61 50.07 39.03 REMARK 500 LYS C 18 59.41 36.37 REMARK 500 SER C 31 -1.96 69.48 REMARK 500 ASP C 73 -169.50 -101.96 REMARK 500 GLU D 65 75.45 71.45 REMARK 500 SER E 31 -0.51 73.83 REMARK 500 ALA E 52 64.97 -115.41 REMARK 500 GLU F 65 102.98 65.22 REMARK 500 SER G 31 -0.91 72.87 REMARK 500 GLU H 65 65.75 77.24 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 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD2 REMARK 620 2 ASP A 98 OD1 112.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 7 OD2 REMARK 620 2 ASP C 98 OD1 130.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 7 OD2 REMARK 620 2 HOH E 316 O 100.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA G 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP G 7 OD2 REMARK 620 2 ASP G 98 OD1 127.6 REMARK 620 N 1 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA G 201 DBREF 6IFC A 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFC B 46 67 UNP Q7CPV2 VAPB_SALTY 46 67 DBREF 6IFC C 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFC D 39 67 UNP Q7CPV2 VAPB_SALTY 39 67 DBREF 6IFC E 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFC F 46 67 UNP Q7CPV2 VAPB_SALTY 46 67 DBREF 6IFC G 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFC H 39 67 UNP Q7CPV2 VAPB_SALTY 39 67 SEQRES 1 A 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 A 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 A 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 A 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 A 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 A 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 A 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 A 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 A 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 A 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 A 132 TRP CYS SEQRES 1 B 22 SER TRP ASP SER TRP PHE ASP GLY GLU GLY ALA SER THR SEQRES 2 B 22 ASP PHE MET SER THR ARG GLU GLN PRO SEQRES 1 C 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 C 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 C 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 C 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 C 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 C 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 C 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 C 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 C 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 C 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 C 132 TRP CYS SEQRES 1 D 29 ILE ILE THR PRO VAL GLY GLU SER TRP ASP SER TRP PHE SEQRES 2 D 29 ASP GLY GLU GLY ALA SER THR ASP PHE MET SER THR ARG SEQRES 3 D 29 GLU GLN PRO SEQRES 1 E 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 E 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 E 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 E 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 E 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 E 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 E 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 E 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 E 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 E 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 E 132 TRP CYS SEQRES 1 F 22 SER TRP ASP SER TRP PHE ASP GLY GLU GLY ALA SER THR SEQRES 2 F 22 ASP PHE MET SER THR ARG GLU GLN PRO SEQRES 1 G 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 G 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 G 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 G 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 G 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 G 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 G 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 G 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 G 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 G 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 G 132 TRP CYS SEQRES 1 H 29 ILE ILE THR PRO VAL GLY GLU SER TRP ASP SER TRP PHE SEQRES 2 H 29 ASP GLY GLU GLY ALA SER THR ASP PHE MET SER THR ARG SEQRES 3 H 29 GLU GLN PRO HET CA A 201 1 HET CA C 201 1 HET CA E 201 1 HET CA G 201 1 HETNAM CA CALCIUM ION FORMUL 9 CA 4(CA 2+) FORMUL 13 HOH *206(H2 O) HELIX 1 AA1 ASP A 7 LYS A 18 1 12 HELIX 2 AA2 PRO A 19 ASN A 29 1 11 HELIX 3 AA3 SER A 37 SER A 50 1 14 HELIX 4 AA4 ALA A 52 ARG A 66 1 15 HELIX 5 AA5 ASP A 73 LYS A 90 1 18 HELIX 6 AA6 GLY A 95 ARG A 108 1 14 HELIX 7 AA7 ASN A 116 GLU A 121 1 6 HELIX 8 AA8 TRP B 47 ASP B 52 1 6 HELIX 9 AA9 ASP C 7 LYS C 18 1 12 HELIX 10 AB1 PRO C 19 ASN C 29 1 11 HELIX 11 AB2 SER C 37 SER C 50 1 14 HELIX 12 AB3 ALA C 52 SER C 65 1 14 HELIX 13 AB4 ASP C 73 GLY C 91 1 19 HELIX 14 AB5 GLY C 95 ARG C 108 1 14 HELIX 15 AB6 ASN C 116 ARG C 122 1 7 HELIX 16 AB7 SER D 46 ASP D 52 1 7 HELIX 17 AB8 ASP E 7 LYS E 18 1 12 HELIX 18 AB9 PRO E 19 ASN E 29 1 11 HELIX 19 AC1 SER E 37 SER E 50 1 14 HELIX 20 AC2 ALA E 52 ARG E 66 1 15 HELIX 21 AC3 ASP E 73 GLY E 91 1 19 HELIX 22 AC4 GLY E 95 ARG E 108 1 14 HELIX 23 AC5 ASN E 116 GLU E 121 1 6 HELIX 24 AC6 TRP F 47 ASP F 52 1 6 HELIX 25 AC7 ASP G 7 LYS G 18 1 12 HELIX 26 AC8 PRO G 19 ASN G 29 1 11 HELIX 27 AC9 SER G 37 SER G 50 1 14 HELIX 28 AD1 ALA G 52 SER G 65 1 14 HELIX 29 AD2 ASP G 73 GLY G 91 1 19 HELIX 30 AD3 GLY G 95 ARG G 108 1 14 HELIX 31 AD4 ASN G 116 GLU G 121 1 6 HELIX 32 AD5 SER H 46 GLY H 53 1 8 SHEET 1 AA110 GLU A 68 LEU A 70 0 SHEET 2 AA110 MET A 33 SER A 36 1 N ILE A 35 O LEU A 70 SHEET 3 AA110 PHE A 4 LEU A 6 1 N LEU A 6 O CYS A 34 SHEET 4 AA110 VAL A 111 VAL A 113 1 O VAL A 111 N MET A 5 SHEET 5 AA110 ARG A 127 GLU A 129 1 O ARG A 127 N VAL A 112 SHEET 6 AA110 ILE E 128 ASP E 130 1 O ASP E 130 N ILE A 128 SHEET 7 AA110 VAL E 111 VAL E 113 1 N VAL E 112 O GLU E 129 SHEET 8 AA110 PHE E 4 LEU E 6 1 N MET E 5 O VAL E 111 SHEET 9 AA110 MET E 33 SER E 36 1 O CYS E 34 N LEU E 6 SHEET 10 AA110 GLU E 68 LEU E 70 1 O LEU E 70 N ILE E 35 SHEET 1 AA2 5 GLU C 68 LEU C 70 0 SHEET 2 AA2 5 MET C 33 SER C 36 1 N ILE C 35 O LEU C 70 SHEET 3 AA2 5 PHE C 4 LEU C 6 1 N LEU C 6 O CYS C 34 SHEET 4 AA2 5 VAL C 111 VAL C 113 1 O VAL C 111 N MET C 5 SHEET 5 AA2 5 ILE C 128 GLU C 129 1 O GLU C 129 N VAL C 112 SHEET 1 AA3 5 GLU G 68 LEU G 70 0 SHEET 2 AA3 5 MET G 33 SER G 36 1 N ILE G 35 O LEU G 70 SHEET 3 AA3 5 PHE G 4 LEU G 6 1 N LEU G 6 O CYS G 34 SHEET 4 AA3 5 VAL G 111 VAL G 113 1 O VAL G 111 N MET G 5 SHEET 5 AA3 5 ILE G 128 GLU G 129 1 O GLU G 129 N VAL G 112 LINK OD2 ASP A 7 CA CA A 201 1555 1555 2.74 LINK OD1 ASP A 98 CA CA A 201 1555 1555 2.64 LINK OD2 ASP C 7 CA CA C 201 1555 1555 2.57 LINK OD1 ASP C 98 CA CA C 201 1555 1555 2.99 LINK OD2 ASP E 7 CA CA E 201 1555 1555 2.89 LINK CA CA E 201 O HOH E 316 1555 1555 2.99 LINK OD2 ASP G 7 CA CA G 201 1555 1555 2.88 LINK OD1 ASP G 98 CA CA G 201 1555 1555 2.78 SITE 1 AC1 5 ASP A 7 THR A 8 ASP A 98 ILE A 101 SITE 2 AC1 5 ARG B 64 SITE 1 AC2 5 ASP C 7 THR C 8 ASN C 9 ASP C 98 SITE 2 AC2 5 ARG D 64 SITE 1 AC3 6 ASP E 7 THR E 8 ASN E 9 ASP E 98 SITE 2 AC3 6 HOH E 316 ARG F 64 SITE 1 AC4 5 ASP G 7 THR G 8 ASN G 9 ASP G 98 SITE 2 AC4 5 ARG H 64 CRYST1 53.956 114.942 53.998 90.00 114.12 90.00 P 1 21 1 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 0.018534 0.000000 0.008299 0.00000 SCALE2 0.000000 0.008700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020291 0.00000