HEADER PROTEIN BINDING 19-AUG-14 4R4T TITLE CRYSTAL STRUCTURE OF RPA70N IN COMPLEX WITH 5-(4-((4-(5-CARBOXYFURAN- TITLE 2 2-YL)PHENYLTHIOAMIDO)METHYL)PHENYL)-1-(3,4-DICHLOROPHENYL)-1H- TITLE 3 PYRAZOLE-3-CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP 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, REPLICATION PROTEIN A 70 KDA COMPND 7 DNA-BINDING SUBUNIT, N-TERMINALLY PROCESSED; COMPND 8 ENGINEERED: YES; COMPND 9 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS OB-FOLD, PROTEIN-PROTEIN INTERACTION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.D.FELDKAMP,A.G.WATERSON,J.P.KENNEDY,J.D.PATRONE,N.F.PELZ,A.O.FRANK, AUTHOR 2 B.VANGAMUDI,E.M.SOUSA-FAGUNDES,O.W.ROSSANESE,S.W.FESIK,W.J.CHAZIN REVDAT 3 20-SEP-23 4R4T 1 REMARK SEQADV REVDAT 2 11-MAR-15 4R4T 1 JRNL REVDAT 1 19-NOV-14 4R4T 0 JRNL AUTH A.G.WATERSON,J.P.KENNEDY,J.D.PATRONE,N.F.PELZ,M.D.FELDKAMP, JRNL AUTH 2 A.O.FRANK,B.VANGAMUDI,E.M.SOUZA-FAGUNDES,O.W.ROSSANESE, JRNL AUTH 3 W.J.CHAZIN,S.W.FESIK JRNL TITL DIPHENYLPYRAZOLES AS REPLICATION PROTEIN A INHIBITORS. JRNL REF ACS MED CHEM LETT V. 6 140 2015 JRNL REFN ISSN 1948-5875 JRNL PMID 25699140 JRNL DOI 10.1021/ML5003629 REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29414 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1497 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 27.0131 - 2.8457 0.99 2697 129 0.1615 0.1848 REMARK 3 2 2.8457 - 2.2591 1.00 2596 130 0.1416 0.1818 REMARK 3 3 2.2591 - 1.9736 1.00 2573 140 0.1107 0.1510 REMARK 3 4 1.9736 - 1.7932 1.00 2529 132 0.1078 0.1423 REMARK 3 5 1.7932 - 1.6647 1.00 2501 150 0.1131 0.1534 REMARK 3 6 1.6647 - 1.5666 1.00 2521 139 0.1213 0.1471 REMARK 3 7 1.5666 - 1.4881 1.00 2522 122 0.1305 0.2127 REMARK 3 8 1.4881 - 1.4233 1.00 2496 130 0.1392 0.1917 REMARK 3 9 1.4233 - 1.3686 1.00 2536 121 0.1518 0.1964 REMARK 3 10 1.3686 - 1.3213 1.00 2467 143 0.1653 0.2363 REMARK 3 11 1.3213 - 1.2800 1.00 2479 161 0.1797 0.2021 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.40 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 : 0.010 1070 REMARK 3 ANGLE : 1.443 1473 REMARK 3 CHIRALITY : 0.082 173 REMARK 3 PLANARITY : 0.006 191 REMARK 3 DIHEDRAL : 19.860 445 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 4R4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : SI(100) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 27.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 18.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45700 REMARK 200 FOR SHELL : 2.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: PDB ENTRY 4IPC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 200 MM CALCIUM ACETATE, REMARK 280 20% PEG 8000, PH 6.5, VAPOR DIFFUSION, SITTING 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 19.09500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.96000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.09500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.96000 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 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 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 A 406 O HOH A 407 2.10 REMARK 500 O HOH A 404 O HOH A 405 2.16 REMARK 500 O HOH A 351 O HOH A 380 2.18 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 SER A 55 31.42 -92.13 REMARK 500 ASN A 74 -15.47 93.51 REMARK 500 VAL A 108 -61.36 -104.86 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 3J0 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R4C RELATED DB: PDB REMARK 900 RELATED ID: 4R4I RELATED DB: PDB REMARK 900 RELATED ID: 4R4O RELATED DB: PDB REMARK 900 RELATED ID: 4R4Q RELATED DB: PDB DBREF 4R4T A 1 120 UNP P27694 RFA1_HUMAN 1 120 SEQADV 4R4T GLY A -2 UNP P27694 EXPRESSION TAG SEQADV 4R4T SER A -1 UNP P27694 EXPRESSION TAG SEQADV 4R4T HIS A 0 UNP P27694 EXPRESSION TAG SEQADV 4R4T 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 3J0 A 201 40 HETNAM 3J0 5-{4-[({[4-(5-CARBOXYFURAN-2-YL) HETNAM 2 3J0 PHENYL]CARBONOTHIOYL}AMINO)METHYL]PHENYL}-1-(3,4- HETNAM 3 3J0 DICHLOROPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC ACID FORMUL 2 3J0 C29 H19 CL2 N3 O5 S FORMUL 3 HOH *120(H2 O) HELIX 1 1 HIS A 0 LEU A 5 5 6 HELIX 2 2 GLY A 8 GLN A 15 1 8 HELIX 3 3 LEU A 62 GLU A 68 1 7 HELIX 4 4 SER A 104 GLY A 109 1 6 SHEET 1 A 7 VAL A 116 PRO A 117 0 SHEET 2 A 7 ASN A 51 LEU A 58 1 N THR A 52 O VAL A 116 SHEET 3 A 7 ARG A 92 LYS A 103 1 O VAL A 94 N SER A 55 SHEET 4 A 7 VAL A 76 THR A 86 -1 N ILE A 83 O ILE A 95 SHEET 5 A 7 ILE A 24 PRO A 32 -1 N LEU A 25 O CYS A 77 SHEET 6 A 7 TYR A 42 SER A 47 -1 O LEU A 45 N ILE A 28 SHEET 7 A 7 ASN A 51 LEU A 58 -1 O LEU A 53 N MET A 46 SITE 1 AC1 18 ILE A 33 THR A 34 ARG A 41 ARG A 43 SITE 2 AC1 18 SER A 55 ALA A 59 THR A 60 ASN A 85 SITE 3 AC1 18 LEU A 87 ARG A 91 ILE A 95 MET A 97 SITE 4 AC1 18 HOH A 312 HOH A 326 HOH A 355 HOH A 384 SITE 5 AC1 18 HOH A 392 HOH A 416 CRYST1 38.190 53.920 54.120 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 0.026185 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018477 0.00000