HEADER REPLICATION 10-MAR-14 4PTA TITLE STRUCTURE OF MDR INITIATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION INITIATOR PROTEIN; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 367830; SOURCE 4 STRAIN: USA300; SOURCE 5 GENE: REPA, SAUSA300_PUSA030001; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INITIATION, REPLICATION, MULTIDRUG RESISTANCE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 3 28-FEB-24 4PTA 1 REMARK REVDAT 2 23-JUL-14 4PTA 1 JRNL REVDAT 1 25-JUN-14 4PTA 0 JRNL AUTH M.A.SCHUMACHER,N.K.TONTHAT,S.M.KWONG,N.B.CHINNAM,M.A.LIU, JRNL AUTH 2 R.A.SKURRAY,N.FIRTH JRNL TITL MECHANISM OF STAPHYLOCOCCAL MULTIRESISTANCE PLASMID JRNL TITL 2 REPLICATION ORIGIN ASSEMBLY BY THE REPA PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 9121 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24927575 JRNL DOI 10.1073/PNAS.1406065111 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 5116 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 511 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 23.6236 - 4.1223 0.89 1102 122 0.2191 0.2484 REMARK 3 2 4.1223 - 3.2747 1.00 1177 131 0.1891 0.2549 REMARK 3 3 3.2747 - 2.8616 1.00 1169 130 0.2456 0.2863 REMARK 3 4 2.8616 - 2.6003 1.00 1157 128 0.3062 0.4808 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.45 REMARK 3 B_SOL : 63.92 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.52090 REMARK 3 B22 (A**2) : 4.52090 REMARK 3 B33 (A**2) : -9.04180 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.003 1038 REMARK 3 ANGLE : 0.648 1402 REMARK 3 CHIRALITY : 0.042 159 REMARK 3 PLANARITY : 0.002 177 REMARK 3 DIHEDRAL : 17.507 396 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 4PTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-12 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5166 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 67.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.44 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 REMARK 200 R SYM FOR SHELL (I) : 0.33200 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M CITRATE, PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 275K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 50.73000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 50.73000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.39000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.69500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.73000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.08500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.08500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.73000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.69500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 50.73000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.39000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 50.73000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 31.39000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 50.73000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 47.08500 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 15.69500 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 50.73000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 15.69500 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 47.08500 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 50.73000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 50.73000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 31.39000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 D 1 REMARK 465 SER D 2 REMARK 465 LYS D 3 REMARK 465 GLN D 100 REMARK 465 GLY D 101 REMARK 465 LEU D 102 REMARK 465 ASN D 103 REMARK 465 LYS D 104 REMARK 465 VAL D 130 REMARK 465 GLU D 131 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 D 99 CG CD NE CZ NH1 NH2 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 O HOH D 214 O HOH D 217 2.16 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 THR D 25 -38.25 -134.97 REMARK 500 ASN D 53 4.92 -67.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PQK RELATED DB: PDB REMARK 900 RELATED ID: 4PT7 RELATED DB: PDB REMARK 900 RELATED ID: 4PQL RELATED DB: PDB DBREF 4PTA D 1 131 UNP Q2FDD7 Q2FDD7_STAA3 1 131 SEQRES 1 D 131 MET SER LYS GLN PHE PHE THR VAL GLU GLU ASN TYR LYS SEQRES 2 D 131 GLU ARG PHE TYR GLN LEU PRO LYS VAL PHE PHE THR ASN SEQRES 3 D 131 PRO ASN TYR LYS ASP LEU SER ASN ASP ALA LYS ILE ALA SEQRES 4 D 131 TYR ALA ILE LEU ARG ASP ARG LEU GLN LEU SER ILE LYS SEQRES 5 D 131 ASN ASN TRP ILE ASP THR GLU GLY ASN ILE TYR PHE ILE SEQRES 6 D 131 TYR THR VAL ALA ASP LEU GLU VAL ILE LEU ASN CYS GLY SEQRES 7 D 131 ASN LYS LYS ILE THR LYS ILE LYS LYS GLU LEU GLU ASN SEQRES 8 D 131 VAL ASP LEU LEU ILE GLN LYS ARG GLN GLY LEU ASN LYS SEQRES 9 D 131 PRO ASN LEU LEU TYR LEU LEU LYS PRO ALA ILE THR LYS SEQRES 10 D 131 ASN ASP ILE TYR GLU ILE ASP LYS ALA GLU ASN GLU VAL SEQRES 11 D 131 GLU FORMUL 2 HOH *32(H2 O) HELIX 1 1 THR D 7 GLU D 14 1 8 HELIX 2 2 PRO D 20 THR D 25 5 6 HELIX 3 3 ASN D 26 ASP D 31 1 6 HELIX 4 4 SER D 33 ASP D 45 1 13 HELIX 5 5 ARG D 46 ASN D 53 1 8 HELIX 6 6 THR D 67 LEU D 75 1 9 HELIX 7 7 GLY D 78 VAL D 92 1 15 HELIX 8 8 THR D 116 ASN D 128 1 13 SHEET 1 A 2 LEU D 95 GLN D 97 0 SHEET 2 A 2 LEU D 108 LEU D 110 -1 O TYR D 109 N ILE D 96 CRYST1 101.460 101.460 62.780 90.00 90.00 90.00 I 41 2 2 16 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 0.009856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015929 0.00000