HEADER TOXIN 09-SEP-09 3JRZ TITLE CCDBVFI-FORMII-PH5.6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CCDB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO FISCHERI; SOURCE 3 ORGANISM_TAXID: 668; SOURCE 4 GENE: CCDB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B462; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKK223-3 KEYWDS ALPHA+BETA, SH3 DOMAIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR N.DE JONGE,L.BUTS,R.LORIS REVDAT 3 01-NOV-23 3JRZ 1 REMARK REVDAT 2 23-FEB-10 3JRZ 1 JRNL REVDAT 1 01-DEC-09 3JRZ 0 JRNL AUTH N.DE JONGE,W.HOHLWEG,A.GARCIA-PINO,M.RESPONDEK,L.BUTS, JRNL AUTH 2 S.HAESAERTS,J.LAH,K.ZANGGER,R.LORIS JRNL TITL STRUCTURAL AND THERMODYNAMIC CHARACTERIZATION OF VIBRIO JRNL TITL 2 FISCHERI CCDB JRNL REF J.BIOL.CHEM. V. 285 5606 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 19959472 JRNL DOI 10.1074/JBC.M109.068429 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.DE JONGE,L.BUTS,J.VANGELOOVEN,N.MINE,L.VAN MELDEREN, REMARK 1 AUTH 2 L.WYNS,R.LORIS REMARK 1 TITL PURIFICATION AND CRYSTALLIZATION OF VIBRIO FISCHERI CCDB AND REMARK 1 TITL 2 ITS COMPLEXES WITH FRAGMENTS OF GYRASE AND CCDA REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 63 356 2007 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 17401216 REMARK 1 DOI 10.1107/S1744309107012092 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 475 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 18.7775 - 2.4507 1.00 3158 155 0.1783 0.1973 REMARK 3 2 2.4507 - 1.9459 1.00 3121 159 0.1429 0.1964 REMARK 3 3 1.9459 - 1.7001 1.00 3108 161 0.1655 0.2030 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 72.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04400 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.11400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.18800 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 785 REMARK 3 ANGLE : 1.395 1074 REMARK 3 CHIRALITY : 0.115 136 REMARK 3 PLANARITY : 0.008 136 REMARK 3 DIHEDRAL : 17.952 283 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3JRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8162 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9956 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.310 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 22.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.23700 REMARK 200 R SYM FOR SHELL (I) : 0.23700 REMARK 200 FOR SHELL : 8.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3JSC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM CITRATE PH5.6, 2% REMARK 280 POLYETHYLENEIMINE, 500MM NACL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.25300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.81200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.25300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.81200 REMARK 290 SMTRY3 4 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: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 REMARK 465 LYS A 48 REMARK 465 LYS A 49 REMARK 465 ALA A 50 REMARK 465 PRO A 51 REMARK 465 SER A 52 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 8 CE NZ REMARK 470 ASN A 31 OD1 ND2 REMARK 470 LEU A 46 CG CD1 CD2 REMARK 470 ASP A 47 CB CG OD1 OD2 REMARK 470 HIS A 53 ND1 CD2 CE1 NE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 ILE A 105 CD1 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 PHE A 4 -0.11 82.99 REMARK 500 GLU A 82 76.00 67.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VUB RELATED DB: PDB REMARK 900 CCDB DIMER REMARK 900 RELATED ID: 2VUB RELATED DB: PDB REMARK 900 CCDB DIMER REMARK 900 RELATED ID: 3VUB RELATED DB: PDB REMARK 900 CCDB DIMER REMARK 900 RELATED ID: 4VUB RELATED DB: PDB REMARK 900 CCDB DIMER REMARK 900 RELATED ID: 3JSC RELATED DB: PDB REMARK 900 CCDBVFI STRUCTURE PH7.0 DBREF 3JRZ A 1 105 UNP Q84B82 Q84B82_VIBFI 1 105 SEQRES 1 A 105 MET SER GLN PHE THR LEU TYR LYS ASN LYS ASP LYS SER SEQRES 2 A 105 SER ALA LYS THR TYR PRO TYR PHE VAL ASP VAL GLN SER SEQRES 3 A 105 ASP LEU LEU ASP ASN LEU ASN THR ARG LEU VAL ILE PRO SEQRES 4 A 105 LEU THR PRO ILE GLU LEU LEU ASP LYS LYS ALA PRO SER SEQRES 5 A 105 HIS LEU CYS PRO THR ILE HIS ILE ASP GLU GLY ASP PHE SEQRES 6 A 105 ILE MET LEU THR GLN GLN MET THR SER VAL PRO VAL LYS SEQRES 7 A 105 ILE LEU SER GLU PRO VAL ASN GLU LEU SER THR PHE ARG SEQRES 8 A 105 ASN GLU ILE ILE ALA ALA ILE ASP PHE LEU ILE THR GLY SEQRES 9 A 105 ILE FORMUL 2 HOH *73(H2 O) HELIX 1 1 SER A 26 ASP A 30 5 5 HELIX 2 2 GLU A 44 LEU A 46 5 3 HELIX 3 3 THR A 69 MET A 72 5 4 HELIX 4 4 LYS A 78 LEU A 80 5 3 HELIX 5 5 PHE A 90 GLY A 104 1 15 SHEET 1 A 4 THR A 57 ILE A 60 0 SHEET 2 A 4 GLY A 63 MET A 67 -1 O PHE A 65 N ILE A 58 SHEET 3 A 4 THR A 34 PRO A 42 -1 N THR A 41 O ILE A 66 SHEET 4 A 4 THR A 73 PRO A 76 -1 O THR A 73 N VAL A 37 SHEET 1 B 6 THR A 57 ILE A 60 0 SHEET 2 B 6 GLY A 63 MET A 67 -1 O PHE A 65 N ILE A 58 SHEET 3 B 6 THR A 34 PRO A 42 -1 N THR A 41 O ILE A 66 SHEET 4 B 6 TYR A 20 ASP A 23 -1 N VAL A 22 O ILE A 38 SHEET 5 B 6 THR A 5 LYS A 8 -1 N TYR A 7 O PHE A 21 SHEET 6 B 6 PRO A 83 GLU A 86 -1 O ASN A 85 N LEU A 6 CRYST1 58.506 43.624 37.489 90.00 110.01 90.00 C 1 2 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 0.017092 0.000000 0.006225 0.00000 SCALE2 0.000000 0.022923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028389 0.00000