HEADER PROTEIN BINDING/INHIBITOR 12-OCT-15 5E7N TITLE CRYSTAL STRUCTURE OF RPA70N IN COMPLEX WITH VU0085636 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-120; COMPND 5 SYNONYM: RP-A P70,REPLICATION FACTOR A PROTEIN 1,RF-A PROTEIN 1, COMPND 6 SINGLE-STRANDED DNA-BINDING PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS INHIBITOR, COMPLEX, PROTEIN BINDING-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.A.GILSTON,J.D.PATRONE,N.F.PELZ,B.S.BATES,E.M.SOUZA-FAGUNDES, AUTHOR 2 B.VANGAMUDI,D.CAMPER,A.KUZNETSOV,C.F.BROWNING,M.D.FELDKAMP, AUTHOR 3 E.T.OLEJNICZAK,O.W.ROSSANESE,A.G.WATERSON,S.W.FESIK,W.J.CHAZIN REVDAT 5 27-SEP-23 5E7N 1 REMARK REVDAT 4 04-DEC-19 5E7N 1 REMARK REVDAT 3 20-SEP-17 5E7N 1 REMARK REVDAT 2 04-MAY-16 5E7N 1 JRNL REVDAT 1 27-JAN-16 5E7N 0 JRNL AUTH J.D.PATRONE,N.F.PELZ,B.S.BATES,E.M.SOUZA-FAGUNDES, JRNL AUTH 2 B.VANGAMUDI,D.V.CAMPER,A.G.KUZNETSOV,C.F.BROWNING, JRNL AUTH 3 M.D.FELDKAMP,A.O.FRANK,B.A.GILSTON,E.T.OLEJNICZAK, JRNL AUTH 4 O.W.ROSSANESE,A.G.WATERSON,W.J.CHAZIN,S.W.FESIK JRNL TITL IDENTIFICATION AND OPTIMIZATION OF ANTHRANILIC ACID BASED JRNL TITL 2 INHIBITORS OF REPLICATION PROTEIN A. JRNL REF CHEMMEDCHEM V. 11 893 2016 JRNL REFN ESSN 1860-7187 JRNL PMID 26748787 JRNL DOI 10.1002/CMDC.201500479 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 34513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1740 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 31.4847 - 2.7697 0.95 2796 135 0.1984 0.2289 REMARK 3 2 2.7697 - 2.1985 1.00 2828 151 0.1844 0.2074 REMARK 3 3 2.1985 - 1.9207 1.00 2785 145 0.1688 0.1711 REMARK 3 4 1.9207 - 1.7451 1.00 2760 138 0.1849 0.2030 REMARK 3 5 1.7451 - 1.6200 1.00 2765 137 0.1902 0.2197 REMARK 3 6 1.6200 - 1.5245 1.00 2728 155 0.1971 0.1986 REMARK 3 7 1.5245 - 1.4481 1.00 2735 165 0.2024 0.2229 REMARK 3 8 1.4481 - 1.3851 1.00 2731 138 0.2125 0.2115 REMARK 3 9 1.3851 - 1.3318 1.00 2717 123 0.2190 0.2379 REMARK 3 10 1.3318 - 1.2858 1.00 2742 149 0.2296 0.2478 REMARK 3 11 1.2858 - 1.2456 0.99 2673 154 0.2464 0.2546 REMARK 3 12 1.2456 - 1.2100 0.93 2513 150 0.3151 0.3526 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.410 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) : 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 : 0.006 1049 REMARK 3 ANGLE : 1.206 1434 REMARK 3 CHIRALITY : 0.066 167 REMARK 3 PLANARITY : 0.005 186 REMARK 3 DIHEDRAL : 12.980 417 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): -7.2183 -8.1622 11.2021 REMARK 3 T TENSOR REMARK 3 T11: 0.0680 T22: 0.0705 REMARK 3 T33: 0.0772 T12: 0.0095 REMARK 3 T13: -0.0110 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.2570 L22: 1.2529 REMARK 3 L33: 2.0075 L12: -0.1636 REMARK 3 L13: -0.3291 L23: 0.1106 REMARK 3 S TENSOR REMARK 3 S11: 0.0212 S12: -0.0466 S13: -0.0268 REMARK 3 S21: 0.0952 S22: 0.0040 S23: -0.0084 REMARK 3 S31: 0.0103 S32: -0.0378 S33: -0.0242 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 5E7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : GRAPHITE 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 708 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 708 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34513 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 31.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4R4T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 200 MM CALCIUM ACETATE, REMARK 280 20% PEG 8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K 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 19.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.24000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.24000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.63000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 55 34.42 -98.93 REMARK 500 ASN A 74 -15.84 93.48 REMARK 500 VAL A 108 -60.15 -95.64 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 5KR A 201 DBREF 5E7N A 1 120 UNP P27694 RFA1_HUMAN 1 120 SEQADV 5E7N GLY A -2 UNP P27694 EXPRESSION TAG SEQADV 5E7N SER A -1 UNP P27694 EXPRESSION TAG SEQADV 5E7N HIS A 0 UNP P27694 EXPRESSION TAG SEQADV 5E7N 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 HET 5KR A 201 30 HETNAM 5KR 2-({3-[(4-BROMOPHENYL)SULFAMOYL]-4- HETNAM 2 5KR METHYLBENZOYL}AMINO)BENZOIC ACID FORMUL 2 5KR C21 H17 BR N2 O5 S FORMUL 3 HOH *70(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 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 SITE 1 AC1 10 ARG A 41 ARG A 43 MET A 57 ILE A 83 SITE 2 AC1 10 ASN A 85 LEU A 87 VAL A 93 ILE A 95 SITE 3 AC1 10 HOH A 301 HOH A 308 CRYST1 38.560 53.260 54.480 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 0.025934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018355 0.00000