HEADER DNA BINDING PROTEIN 28-NOV-16 5WQV TITLE CRYSTAL STRUCTURE OF PRIB MUTANT - S55A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRIMOSOMAL REPLICATION PROTEIN N; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 595496; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PRIB, BWG_3913; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS DNA BINDING PROTEIN, BACTERIAL DNA REPLICATION, OB-FOLD, S55A MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR S.FUJIYAMA,M.SHIROISHI,T.KATAYAMA,Y.ABE,T.UEDA REVDAT 2 12-JUN-19 5WQV 1 JRNL REVDAT 1 29-NOV-17 5WQV 0 JRNL AUTH S.FUJIYAMA,Y.ABE,M.SHIROISHI,Y.IKEDA,T.UEDA JRNL TITL INSIGHT INTO THE INTERACTION BETWEEN PRIB AND DNAT ON JRNL TITL 2 BACTERIAL DNA REPLICATION RESTART: SIGNIFICANCE OF THE JRNL TITL 3 RESIDUES ON PRIB DIMER INTERFACE AND HIGHLY ACIDIC REGION ON JRNL TITL 4 DNAT. JRNL REF BIOCHIM BIOPHYS ACTA V.1867 367 2019 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 30659961 JRNL DOI 10.1016/J.BBAPAP.2019.01.008 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 13581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 665 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 2.1200 - 1.9700 0.99 2602 125 0.2226 0.3008 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 5WQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1300002227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG 400, AMMONIUM SULFATE, PH REMARK 280 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.94000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.54750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.55250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.54750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.94000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.55250 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 MET A 1 REMARK 465 ALA A 83 REMARK 465 LYS A 84 REMARK 465 ASN A 85 REMARK 465 GLY A 86 REMARK 465 LEU A 87 REMARK 465 ASP A 101 REMARK 465 SER A 102 REMARK 465 GLY A 103 REMARK 465 ASP A 104 REMARK 465 MET B 1 REMARK 465 LYS B 82 REMARK 465 ALA B 83 REMARK 465 LYS B 84 REMARK 465 ASN B 85 REMARK 465 GLY B 86 REMARK 465 LEU B 87 REMARK 465 SER B 88 REMARK 465 ILE B 100 REMARK 465 ASP B 101 REMARK 465 SER B 102 REMARK 465 GLY B 103 REMARK 465 ASP B 104 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 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 13 CD NE CZ NH1 NH2 REMARK 470 LYS A 18 CD CE NZ REMARK 470 GLN A 28 CG CD OE1 NE2 REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 ARG B 13 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 18 CD CE NZ REMARK 470 ILE B 24 CG1 CG2 CD1 REMARK 470 PHE B 42 CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 45 CG CD OE1 NE2 REMARK 470 GLN B 60 CG CD OE1 NE2 REMARK 470 HIS B 64 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 71 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 89 CG CD CE NZ REMARK 470 GLN B 96 CD OE1 NE2 REMARK 470 GLU B 98 CG CD OE1 OE2 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 3 88.12 -150.29 REMARK 500 ASN B 3 85.69 -151.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 5WQV A 1 104 UNP C4ZR78 PRIB_ECOBW 1 104 DBREF 5WQV B 1 104 UNP C4ZR78 PRIB_ECOBW 1 104 SEQADV 5WQV ALA A 55 UNP C4ZR78 SER 55 ENGINEERED MUTATION SEQADV 5WQV ALA B 55 UNP C4ZR78 SER 55 ENGINEERED MUTATION SEQRES 1 A 104 MET THR ASN ARG LEU VAL LEU SER GLY THR VAL CYS ARG SEQRES 2 A 104 ALA PRO LEU ARG LYS VAL SER PRO SER GLY ILE PRO HIS SEQRES 3 A 104 CYS GLN PHE VAL LEU GLU HIS ARG SER VAL GLN GLU GLU SEQRES 4 A 104 ALA GLY PHE HIS ARG GLN ALA TRP CYS GLN MET PRO VAL SEQRES 5 A 104 ILE VAL ALA GLY HIS GLU ASN GLN ALA ILE THR HIS SER SEQRES 6 A 104 ILE THR VAL GLY SER ARG ILE THR VAL GLN GLY PHE ILE SEQRES 7 A 104 SER CYS HIS LYS ALA LYS ASN GLY LEU SER LYS MET VAL SEQRES 8 A 104 LEU HIS ALA GLU GLN ILE GLU LEU ILE ASP SER GLY ASP SEQRES 1 B 104 MET THR ASN ARG LEU VAL LEU SER GLY THR VAL CYS ARG SEQRES 2 B 104 ALA PRO LEU ARG LYS VAL SER PRO SER GLY ILE PRO HIS SEQRES 3 B 104 CYS GLN PHE VAL LEU GLU HIS ARG SER VAL GLN GLU GLU SEQRES 4 B 104 ALA GLY PHE HIS ARG GLN ALA TRP CYS GLN MET PRO VAL SEQRES 5 B 104 ILE VAL ALA GLY HIS GLU ASN GLN ALA ILE THR HIS SER SEQRES 6 B 104 ILE THR VAL GLY SER ARG ILE THR VAL GLN GLY PHE ILE SEQRES 7 B 104 SER CYS HIS LYS ALA LYS ASN GLY LEU SER LYS MET VAL SEQRES 8 B 104 LEU HIS ALA GLU GLN ILE GLU LEU ILE ASP SER GLY ASP FORMUL 3 HOH *97(H2 O) HELIX 1 AA1 ASN A 59 HIS A 64 1 6 HELIX 2 AA2 GLY B 56 GLU B 58 5 3 HELIX 3 AA3 ASN B 59 SER B 65 1 7 SHEET 1 AA112 ASN A 3 VAL A 19 0 SHEET 2 AA112 PRO A 25 GLU A 39 -1 O GLU A 32 N THR A 10 SHEET 3 AA112 PHE A 42 ALA A 55 -1 O MET A 50 N LEU A 31 SHEET 4 AA112 LYS A 89 LEU A 99 1 O LEU A 92 N PRO A 51 SHEET 5 AA112 ARG A 71 HIS A 81 -1 N PHE A 77 O HIS A 93 SHEET 6 AA112 ASN A 3 VAL A 19 -1 N LEU A 5 O GLY A 76 SHEET 7 AA112 ASN B 3 VAL B 19 -1 O ARG B 4 N VAL A 6 SHEET 8 AA112 ARG B 71 SER B 79 -1 O GLY B 76 N LEU B 5 SHEET 9 AA112 VAL B 91 GLU B 98 -1 O HIS B 93 N PHE B 77 SHEET 10 AA112 PHE B 42 VAL B 54 1 N ILE B 53 O ALA B 94 SHEET 11 AA112 PRO B 25 GLU B 39 -1 N HIS B 33 O CYS B 48 SHEET 12 AA112 ASN B 3 VAL B 19 -1 N THR B 10 O GLU B 32 SSBOND 1 CYS A 48 CYS B 80 1555 1555 2.05 SSBOND 2 CYS A 80 CYS B 48 1555 1555 2.04 CRYST1 49.880 59.105 65.095 90.00 90.00 90.00 P 21 21 21 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 0.020048 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016919 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015362 0.00000