HEADER HYDROLASE 30-MAY-16 5K8J TITLE STRUCTURE OF CAULOBACTER CRESCENTUS VAPBC1 (APO FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VAPB FAMILY PROTEIN; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE VAPC; COMPND 7 CHAIN: B, C; COMPND 8 SYNONYM: RNASE VAPC,TOXIN VAPC; COMPND 9 EC: 3.1.-.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER CRESCENTUS; SOURCE 3 ORGANISM_TAXID: 190650; SOURCE 4 STRAIN: ATCC 19089 / CB15; SOURCE 5 GENE: CC_0032; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKW912HB; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: CAULOBACTER CRESCENTUS; SOURCE 12 ORGANISM_TAXID: 190650; SOURCE 13 STRAIN: ATCC 19089 / CB15; SOURCE 14 GENE: VAPC, CC_0031; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 17 EXPRESSION_SYSTEM_VARIANT: B834(DE3); SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PKW912HB KEYWDS PIN DOMAIN, TOXIN-ANTITOXIN, RIBONUCLEASE, DNA-BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.BENDTSEN,K.XU,M.LUCKMANN,D.E.BRODERSEN REVDAT 5 06-NOV-24 5K8J 1 REMARK REVDAT 4 17-JAN-18 5K8J 1 REMARK REVDAT 3 03-MAY-17 5K8J 1 JRNL REVDAT 2 11-JAN-17 5K8J 1 JRNL REVDAT 1 28-DEC-16 5K8J 0 JRNL AUTH K.L.BENDTSEN,K.XU,M.LUCKMANN,K.S.WINTHER,S.A.SHAH, JRNL AUTH 2 C.N.S.PEDERSEN,D.E.BRODERSEN JRNL TITL TOXIN INHIBITION IN C. CRESCENTUS VAPBC1 IS MEDIATED BY A JRNL TITL 2 FLEXIBLE PSEUDO-PALINDROMIC PROTEIN MOTIF AND MODULATED BY JRNL TITL 3 DNA BINDING. JRNL REF NUCLEIC ACIDS RES. V. 45 2875 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 27998932 JRNL DOI 10.1093/NAR/GKW1266 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2152: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 63905 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1975 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 37.3748 - 3.8549 1.00 4746 152 0.1510 0.1591 REMARK 3 2 3.8549 - 3.0602 1.00 4595 145 0.1416 0.1432 REMARK 3 3 3.0602 - 2.6735 1.00 4534 143 0.1545 0.1702 REMARK 3 4 2.6735 - 2.4291 1.00 4499 146 0.1489 0.1617 REMARK 3 5 2.4291 - 2.2550 1.00 4492 145 0.1369 0.1484 REMARK 3 6 2.2550 - 2.1221 1.00 4485 139 0.1444 0.1469 REMARK 3 7 2.1221 - 2.0158 0.99 4440 144 0.1460 0.1502 REMARK 3 8 2.0158 - 1.9281 0.99 4437 144 0.1528 0.1684 REMARK 3 9 1.9281 - 1.8539 0.98 4406 138 0.1698 0.2122 REMARK 3 10 1.8539 - 1.7899 0.97 4330 139 0.1840 0.2178 REMARK 3 11 1.7899 - 1.7339 0.96 4304 137 0.2045 0.2151 REMARK 3 12 1.7339 - 1.6844 0.95 4263 136 0.2191 0.2550 REMARK 3 13 1.6844 - 1.6400 0.95 4205 129 0.2328 0.2365 REMARK 3 14 1.6400 - 1.6000 0.94 4194 138 0.2532 0.2298 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.21 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 : 0.014 3254 REMARK 3 ANGLE : 1.134 4415 REMARK 3 CHIRALITY : 0.171 509 REMARK 3 PLANARITY : 0.008 576 REMARK 3 DIHEDRAL : 18.243 1976 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 20.3497 36.3746 39.8612 REMARK 3 T TENSOR REMARK 3 T11: 0.0801 T22: 0.1198 REMARK 3 T33: 0.1093 T12: -0.0112 REMARK 3 T13: 0.0043 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.1218 L22: 0.5340 REMARK 3 L33: 0.9846 L12: -0.2665 REMARK 3 L13: 0.0883 L23: 0.0233 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: 0.0696 S13: -0.1145 REMARK 3 S21: 0.0020 S22: -0.0306 S23: 0.0101 REMARK 3 S31: 0.0731 S32: 0.0497 S33: 0.0117 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 5K8J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 125126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 37.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14000 REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 M NACL, 0.1 M BIS-TRIS PH 5.5, 5 MM REMARK 280 MGCL2, 5 MM BETA-MERCAPTO ETHANOL, 25% GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.94000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.88000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.88000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.94000 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.0 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 113.82000 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 MSE A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 MSE B 1 REMARK 465 MSE C 1 REMARK 465 MSE D -5 REMARK 465 SER D 64 REMARK 465 VAL D 65 REMARK 465 GLU D 66 REMARK 465 ILE D 67 REMARK 465 ARG D 68 REMARK 465 ASP D 69 REMARK 465 GLU D 70 REMARK 465 ASP D 71 REMARK 465 LEU D 72 REMARK 465 PHE D 73 REMARK 465 PRO D 74 REMARK 465 GLU D 75 REMARK 465 ARG D 76 REMARK 465 PRO D 77 REMARK 465 GLY D 78 REMARK 465 LEU D 79 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH11 ARG A 68 O HOH A 101 1.45 REMARK 500 HG SER C 34 OE1 GLN C 101 1.59 REMARK 500 O HOH A 104 O HOH C 417 2.02 REMARK 500 O HOH A 143 O HOH D 135 2.03 REMARK 500 O THR B 111 N TRP B 128 2.09 REMARK 500 NH1 ARG A 68 O HOH A 101 2.11 REMARK 500 O THR C 111 N TRP C 128 2.11 REMARK 500 O HOH C 413 O HOH C 422 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N ASN D 13 H ASN D 13 4556 0.92 REMARK 500 HH11 ARG C 81 O HOH D 127 5565 1.54 REMARK 500 HE ARG C 81 OD1 ASN D 57 5565 1.59 REMARK 500 N ASN D 13 N ASN D 13 4556 1.83 REMARK 500 O HOH B 317 O HOH C 389 5665 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MSE C 97 SE MSE C 97 CE -0.547 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 VAL C 83 CG1 - CB - CG2 ANGL. DEV. = 12.5 DEGREES REMARK 500 VAL C 83 CG1 - CB - CG2 ANGL. DEV. = 13.2 DEGREES REMARK 500 VAL C 83 CA - CB - CG2 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG D 61 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG D 61 NE - CZ - NH2 ANGL. DEV. = -4.8 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 ASN A 13 51.52 -96.98 REMARK 500 PRO A 77 108.84 -56.61 REMARK 500 ASN B 28 79.56 -102.84 REMARK 500 ASN D 13 46.19 -97.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5L6L RELATED DB: PDB REMARK 900 CONTAINS A DNA-BOUND FORM OF THE VAPBC COMPLEX REMARK 900 RELATED ID: 5L6M RELATED DB: PDB REMARK 900 CONTAINS A MUTATED VERSION OF THE APO, VAPBC COMPLEX DBREF 5K8J A 2 79 UNP Q9AC34 Q9AC34_CAUCR 2 79 DBREF 5K8J B 1 128 UNP Q9AC35 Q9AC35_CAUCR 1 128 DBREF 5K8J C 1 128 UNP Q9AC35 Q9AC35_CAUCR 1 128 DBREF 5K8J D 2 79 UNP Q9AC34 Q9AC34_CAUCR 2 79 SEQADV 5K8J MSE A -5 UNP Q9AC34 INITIATING METHIONINE SEQADV 5K8J HIS A -4 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS A -3 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS A -2 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS A -1 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS A 0 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS A 1 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J MSE D -5 UNP Q9AC34 INITIATING METHIONINE SEQADV 5K8J HIS D -4 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS D -3 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS D -2 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS D -1 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS D 0 UNP Q9AC34 EXPRESSION TAG SEQADV 5K8J HIS D 1 UNP Q9AC34 EXPRESSION TAG SEQRES 1 A 85 MSE HIS HIS HIS HIS HIS HIS ALA ARG ALA THR GLY LYS SEQRES 2 A 85 THR PHE ARG SER GLY ASN SER GLU ALA VAL ARG LEU PRO SEQRES 3 A 85 ARG ASP LEU ALA PHE GLY ALA ASP VAL GLU LEU THR LEU SEQRES 4 A 85 ILE ARG SER GLY ASP VAL LEU THR ILE TYR PRO SER LYS SEQRES 5 A 85 GLY SER ILE ALA ASP LEU VAL ALA THR LEU ASN GLN MSE SEQRES 6 A 85 PRO ARG PRO ASP SER VAL GLU ILE ARG ASP GLU ASP LEU SEQRES 7 A 85 PHE PRO GLU ARG PRO GLY LEU SEQRES 1 B 128 MSE ALA TYR VAL LEU ASP THR ASN VAL ALA ILE HIS LEU SEQRES 2 B 128 ARG ASP GLY ASP PRO GLU VAL THR THR ARG VAL THR ALA SEQRES 3 B 128 LEU ASN GLY ALA ILE LEU LEU SER ILE ILE SER ARG VAL SEQRES 4 B 128 GLU LEU GLU GLY GLY VAL TYR ARG GLU ALA ALA GLN ALA SEQRES 5 B 128 GLY LEU ARG ARG SER ARG LEU ASP VAL MSE LEU LYS VAL SEQRES 6 B 128 LEU PRO VAL LEU ASP PHE ASP GLY ALA ALA ALA ASP GLU SEQRES 7 B 128 TYR ARG ARG ILE VAL GLU SER ALA GLY TYR SER ARG ARG SEQRES 8 B 128 LYS VAL VAL ASP ARG MSE ILE ALA ALA GLN ALA LEU ALA SEQRES 9 B 128 HIS ARG ALA THR PHE VAL THR PHE ASN ALA ASP ASP PHE SEQRES 10 B 128 ARG ASP ILE PRO GLY LEU SER LEU LEU ALA TRP SEQRES 1 C 128 MSE ALA TYR VAL LEU ASP THR ASN VAL ALA ILE HIS LEU SEQRES 2 C 128 ARG ASP GLY ASP PRO GLU VAL THR THR ARG VAL THR ALA SEQRES 3 C 128 LEU ASN GLY ALA ILE LEU LEU SER ILE ILE SER ARG VAL SEQRES 4 C 128 GLU LEU GLU GLY GLY VAL TYR ARG GLU ALA ALA GLN ALA SEQRES 5 C 128 GLY LEU ARG ARG SER ARG LEU ASP VAL MSE LEU LYS VAL SEQRES 6 C 128 LEU PRO VAL LEU ASP PHE ASP GLY ALA ALA ALA ASP GLU SEQRES 7 C 128 TYR ARG ARG ILE VAL GLU SER ALA GLY TYR SER ARG ARG SEQRES 8 C 128 LYS VAL VAL ASP ARG MSE ILE ALA ALA GLN ALA LEU ALA SEQRES 9 C 128 HIS ARG ALA THR PHE VAL THR PHE ASN ALA ASP ASP PHE SEQRES 10 C 128 ARG ASP ILE PRO GLY LEU SER LEU LEU ALA TRP SEQRES 1 D 85 MSE HIS HIS HIS HIS HIS HIS ALA ARG ALA THR GLY LYS SEQRES 2 D 85 THR PHE ARG SER GLY ASN SER GLU ALA VAL ARG LEU PRO SEQRES 3 D 85 ARG ASP LEU ALA PHE GLY ALA ASP VAL GLU LEU THR LEU SEQRES 4 D 85 ILE ARG SER GLY ASP VAL LEU THR ILE TYR PRO SER LYS SEQRES 5 D 85 GLY SER ILE ALA ASP LEU VAL ALA THR LEU ASN GLN MSE SEQRES 6 D 85 PRO ARG PRO ASP SER VAL GLU ILE ARG ASP GLU ASP LEU SEQRES 7 D 85 PHE PRO GLU ARG PRO GLY LEU MODRES 5K8J MSE A 59 MET MODIFIED RESIDUE MODRES 5K8J MSE B 62 MET MODIFIED RESIDUE MODRES 5K8J MSE B 97 MET MODIFIED RESIDUE MODRES 5K8J MSE C 62 MET MODIFIED RESIDUE MODRES 5K8J MSE C 97 MET MODIFIED RESIDUE MODRES 5K8J MSE D 59 MET MODIFIED RESIDUE HET MSE A 59 17 HET MSE B 62 17 HET MSE B 97 17 HET MSE C 62 29 HET MSE C 97 17 HET MSE D 59 17 HET GOL B 201 14 HET GOL C 201 14 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *352(H2 O) HELIX 1 AA1 SER A 48 MSE A 59 1 12 HELIX 2 AA2 ASP B 6 GLY B 16 1 11 HELIX 3 AA3 ASP B 17 LEU B 27 1 11 HELIX 4 AA4 ILE B 35 TYR B 46 1 12 HELIX 5 AA5 GLU B 48 LEU B 66 1 19 HELIX 6 AA6 ASP B 72 GLY B 87 1 16 HELIX 7 AA7 LYS B 92 HIS B 105 1 14 HELIX 8 AA8 ASN B 113 ARG B 118 5 6 HELIX 9 AA9 ASP C 6 ASP C 15 1 10 HELIX 10 AB1 ASP C 17 THR C 25 1 9 HELIX 11 AB2 ILE C 35 TYR C 46 1 12 HELIX 12 AB3 GLN C 51 LEU C 66 1 16 HELIX 13 AB4 ASP C 72 GLY C 87 1 16 HELIX 14 AB5 SER C 89 ARG C 91 5 3 HELIX 15 AB6 LYS C 92 ARG C 106 1 15 HELIX 16 AB7 ASN C 113 ARG C 118 5 6 HELIX 17 AB8 SER D 48 GLN D 58 1 11 SHEET 1 AA1 6 HIS A 1 LYS A 7 0 SHEET 2 AA1 6 GLU D 30 SER D 36 -1 O LEU D 31 N GLY A 6 SHEET 3 AA1 6 VAL D 39 PRO D 44 -1 O TYR D 43 N THR D 32 SHEET 4 AA1 6 VAL A 39 PRO A 44 -1 N ILE A 42 O LEU D 40 SHEET 5 AA1 6 LEU A 31 SER A 36 -1 N THR A 32 O TYR A 43 SHEET 6 AA1 6 HIS D 1 GLY D 6 -1 O GLY D 6 N LEU A 31 SHEET 1 AA2 4 PHE A 9 ARG A 10 0 SHEET 2 AA2 4 GLU A 15 LEU A 19 -1 O ALA A 16 N PHE A 9 SHEET 3 AA2 4 GLU D 15 LEU D 19 -1 O GLU D 15 N LEU A 19 SHEET 4 AA2 4 PHE D 9 ARG D 10 -1 N PHE D 9 O ALA D 16 SHEET 1 AA3 5 VAL B 68 LEU B 69 0 SHEET 2 AA3 5 ILE B 31 SER B 34 1 N LEU B 33 O LEU B 69 SHEET 3 AA3 5 TYR B 3 LEU B 5 1 N TYR B 3 O LEU B 32 SHEET 4 AA3 5 THR B 108 THR B 111 1 O THR B 108 N VAL B 4 SHEET 5 AA3 5 LEU B 125 ALA B 127 1 O LEU B 126 N PHE B 109 SHEET 1 AA4 5 VAL C 68 LEU C 69 0 SHEET 2 AA4 5 ILE C 31 SER C 34 1 N LEU C 33 O LEU C 69 SHEET 3 AA4 5 TYR C 3 LEU C 5 1 N TYR C 3 O LEU C 32 SHEET 4 AA4 5 THR C 108 THR C 111 1 O VAL C 110 N VAL C 4 SHEET 5 AA4 5 SER C 124 ALA C 127 1 O SER C 124 N PHE C 109 LINK C GLN A 58 N MSE A 59 1555 1555 1.33 LINK C MSE A 59 N PRO A 60 1555 1555 1.33 LINK C VAL B 61 N MSE B 62 1555 1555 1.33 LINK C MSE B 62 N LEU B 63 1555 1555 1.33 LINK C ARG B 96 N MSE B 97 1555 1555 1.34 LINK C MSE B 97 N ILE B 98 1555 1555 1.33 LINK C VAL C 61 N MSE C 62 1555 1555 1.33 LINK C MSE C 62 N LEU C 63 1555 1555 1.33 LINK C ARG C 96 N MSE C 97 1555 1555 1.35 LINK C MSE C 97 N ILE C 98 1555 1555 1.34 LINK C GLN D 58 N MSE D 59 1555 1555 1.33 LINK C MSE D 59 N PRO D 60 1555 1555 1.34 CISPEP 1 GLY D 12 ASN D 13 0 -21.94 SITE 1 AC1 8 VAL B 68 ASP B 70 HOH B 339 HOH B 384 SITE 2 AC1 8 ASP C 72 GLY C 73 GLY D 37 HOH D 108 SITE 1 AC2 7 TYR B 3 LEU B 27 ASN B 28 THR C 108 SITE 2 AC2 7 LEU C 125 HOH C 348 HOH C 392 CRYST1 86.290 86.290 113.820 90.00 90.00 120.00 P 31 2 1 12 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 0.011589 0.006691 0.000000 0.00000 SCALE2 0.000000 0.013382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008786 0.00000