PDB Short entry for 5N85 HEADER PROTEIN BINDING 23-FEB-17 5N85 TITLE STRUCTURE OF RPA70N IN COMPLEX WITH PRIMPOL (FRAGMENT 514-525) COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RP-A P70,REPLICATION FACTOR A PROTEIN 1,RF-A PROTEIN 1, COMPND 5 SINGLE-STRANDED DNA-BINDING PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA-DIRECTED PRIMASE/POLYMERASE PROTEIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 514-528; COMPND 12 SYNONYM: HPRIMPOL1,COILED-COIL DOMAIN-CONTAINING PROTEIN 111; COMPND 13 EC: 2.7.7.-; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RPA1, REPA1, RPA70; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, REPLICATION, BASIC CLEFT, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.C.BRISSETT,A.J.DOHERTY REVDAT 3 17-JAN-24 5N85 1 REMARK REVDAT 2 30-AUG-17 5N85 1 REMARK REVDAT 1 07-JUN-17 5N85 0 JRNL AUTH T.A.GUILLIAM,N.C.BRISSETT,A.EHLINGER,B.A.KEEN,P.KOLESAR, JRNL AUTH 2 E.M.TAYLOR,L.J.BAILEY,H.D.LINDSAY,W.J.CHAZIN,A.J.DOHERTY JRNL TITL MOLECULAR BASIS FOR PRIMPOL RECRUITMENT TO REPLICATION FORKS JRNL TITL 2 BY RPA. JRNL REF NAT COMMUN V. 8 15222 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28534480 JRNL DOI 10.1038/NCOMMS15222 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 390 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 31.1215 - 2.8841 1.00 2574 135 0.1731 0.2085 REMARK 3 2 2.8841 - 2.2894 1.00 2463 123 0.2062 0.2359 REMARK 3 3 2.2894 - 2.0001 0.99 2398 132 0.1982 0.2694 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 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 : 0.004 1098 REMARK 3 ANGLE : 0.785 1503 REMARK 3 CHIRALITY : 0.048 182 REMARK 3 PLANARITY : 0.005 196 REMARK 3 DIHEDRAL : 14.582 709 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): 2.6106 -1.1350 -5.2363 REMARK 3 T TENSOR REMARK 3 T11: 0.0831 T22: 0.0772 REMARK 3 T33: 0.0836 T12: -0.0033 REMARK 3 T13: -0.0086 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.3953 L22: 0.4354 REMARK 3 L33: 0.8591 L12: -0.0119 REMARK 3 L13: 0.1350 L23: -0.1386 REMARK 3 S TENSOR REMARK 3 S11: 0.0092 S12: -0.0444 S13: 0.0546 REMARK 3 S21: 0.0405 S22: -0.0395 S23: -0.0102 REMARK 3 S31: -0.1210 S32: 0.0540 S33: 0.0082 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 5N85 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX-HF MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.1.0 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7856 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.073 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.21700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.75100 REMARK 200 R SYM FOR SHELL (I) : 0.75100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 4IPC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE 0.1 M SODIUM REMARK 280 ACETATE 4.5 20 % W/V PEG 3350, PH 4.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.15K 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 18.93000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.31500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.31500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.93000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.54500 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: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 THR B 13 REMARK 465 GLU B 14 REMARK 465 ASP B 15 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 ASN A 37 CG OD1 ND2 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 A 35 -71.81 -111.71 REMARK 500 SER A 38 173.94 179.15 REMARK 500 SER A 55 30.76 -97.61 REMARK 500 SER A 55 30.07 -97.12 REMARK 500 ASN A 74 -17.22 96.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 5N85 A 1 120 UNP P27694 RFA1_HUMAN 1 120 DBREF 5N85 B 1 15 UNP Q96LW4 PRIPO_HUMAN 514 528 SEQADV 5N85 GLY A -2 UNP P27694 EXPRESSION TAG SEQADV 5N85 SER A -1 UNP P27694 EXPRESSION TAG SEQADV 5N85 HIS A 0 UNP P27694 EXPRESSION TAG SEQADV 5N85 ARG A 7 UNP P27694 GLU 7 ENGINEERED MUTATION SEQRES 1 A 123 GLY SER HIS MET VAL GLY GLN LEU SER ARG GLY ALA ILE SEQRES 2 A 123 ALA ALA ILE MET GLN LYS GLY ASP THR ASN ILE LYS PRO SEQRES 3 A 123 ILE LEU GLN VAL ILE ASN ILE ARG PRO ILE THR THR GLY SEQRES 4 A 123 ASN SER PRO PRO ARG TYR ARG LEU LEU MET SER ASP GLY SEQRES 5 A 123 LEU ASN THR LEU SER SER PHE MET LEU ALA THR GLN LEU SEQRES 6 A 123 ASN PRO LEU VAL GLU GLU GLU GLN LEU SER SER ASN CYS SEQRES 7 A 123 VAL CYS GLN ILE HIS ARG PHE ILE VAL ASN THR LEU LYS SEQRES 8 A 123 ASP GLY ARG ARG VAL VAL ILE LEU MET GLU LEU GLU VAL SEQRES 9 A 123 LEU LYS SER ALA GLU ALA VAL GLY VAL LYS ILE GLY ASN SEQRES 10 A 123 PRO VAL PRO TYR ASN GLU SEQRES 1 B 15 ASP ASN GLY ILE ASP ASP ALA TYR PHE LEU GLU ALA THR SEQRES 2 B 15 GLU ASP FORMUL 3 HOH *74(H2 O) HELIX 1 AA1 HIS A 0 LEU A 5 5 6 HELIX 2 AA2 GLY A 8 GLY A 17 1 10 HELIX 3 AA3 LEU A 62 GLU A 68 1 7 HELIX 4 AA4 SER A 104 GLY A 109 1 6 HELIX 5 AA5 ASP B 5 PHE B 9 5 5 SHEET 1 AA1 7 VAL A 116 PRO A 117 0 SHEET 2 AA1 7 ASN A 51 LEU A 58 1 N THR A 52 O VAL A 116 SHEET 3 AA1 7 ARG A 92 LYS A 103 1 O LEU A 96 N MET A 57 SHEET 4 AA1 7 VAL A 76 THR A 86 -1 N ASN A 85 O VAL A 93 SHEET 5 AA1 7 ILE A 24 ILE A 33 -1 N LEU A 25 O CYS A 77 SHEET 6 AA1 7 ARG A 41 SER A 47 -1 O LEU A 45 N ILE A 28 SHEET 7 AA1 7 ASN A 51 LEU A 58 -1 O LEU A 58 N TYR A 42 CRYST1 37.860 53.090 54.630 90.00 90.00 90.00 P 21 21 21 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 0.026413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018305 0.00000