HEADER DNA BINDING PROTEIN/INHIBITOR 21-DEC-12 4IJL TITLE FRAGMENT-BASED DISCOVERY OF PROTEIN-PROTEIN INTERACTION INHIBITORS OF TITLE 2 REPLICATION PROTEIN A 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; 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: REPA1, RPA1, 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, DNA BINDING PROTEIN-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.D.FELDKAMP,J.D.PATRONE,J.P.KENNEDY,A.O.FRANK,B.VANGAMUDI,N.F.PELZ, AUTHOR 2 O.W.ROSSANESE,A.G.WATERSON,S.W.FESIK,W.J.CHAZIN REVDAT 2 20-SEP-23 4IJL 1 REMARK SEQADV REVDAT 1 14-AUG-13 4IJL 0 JRNL AUTH J.D.PATRONE,J.P.KENNEDY,A.O.FRANK,M.D.FELDKAMP,B.VANGAMUDI, JRNL AUTH 2 N.F.PELZ,O.W.ROSSANESE,A.G.WATERSON,W.J.CHAZIN,S.W.FESIK JRNL TITL DISCOVERY OF PROTEIN-PROTEIN INTERACTION INHIBITORS OF JRNL TITL 2 REPLICATION PROTEIN A. JRNL REF ACS MED.CHEM.LETT. V. 4 601 2013 JRNL REFN ISSN 1948-5875 JRNL PMID 23914285 JRNL DOI 10.1021/ML400032Y REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 641 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 38.1302 - 2.9067 0.99 2494 126 0.1750 0.2061 REMARK 3 2 2.9067 - 2.3072 1.00 2390 129 0.2107 0.2540 REMARK 3 3 2.3072 - 2.0156 1.00 2340 133 0.1920 0.2454 REMARK 3 4 2.0156 - 1.8313 1.00 2338 138 0.2127 0.2583 REMARK 3 5 1.8313 - 1.7000 1.00 2317 115 0.2146 0.2658 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.90 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 : 0.014 1037 REMARK 3 ANGLE : 1.688 1415 REMARK 3 CHIRALITY : 0.109 162 REMARK 3 PLANARITY : 0.007 180 REMARK 3 DIHEDRAL : 15.293 417 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): 2.2660 1.6631 5.0758 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.1469 REMARK 3 T33: 0.1481 T12: 0.0086 REMARK 3 T13: 0.0003 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.0900 L22: 1.6538 REMARK 3 L33: 1.2804 L12: 0.3357 REMARK 3 L13: -0.4000 L23: 0.0414 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.0579 S13: -0.0977 REMARK 3 S21: -0.0771 S22: -0.0292 S23: 0.0143 REMARK 3 S31: 0.1183 S32: -0.0365 S33: 0.0208 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 4IJL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076833. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-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) : 0.97857 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15051 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 28.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54800 REMARK 200 FOR SHELL : 3.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8.1_1168 REMARK 200 STARTING MODEL: PDB ENTRY 2B29 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 200 CALCIUM ACETATE, 15% REMARK 280 PEG8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 18.77550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.12950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.78450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.12950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.77550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.78450 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 O18 1EK A 201 O HOH A 318 2.09 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 ASN A 74 -15.73 94.60 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 1EK A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1EK A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IJH RELATED DB: PDB DBREF 4IJL A 1 120 UNP P27694 RFA1_HUMAN 1 120 SEQADV 4IJL GLY A -2 UNP P27694 EXPRESSION TAG SEQADV 4IJL SER A -1 UNP P27694 EXPRESSION TAG SEQADV 4IJL HIS A 0 UNP P27694 EXPRESSION TAG SEQADV 4IJL 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 1EK A 201 26 HET 1EK A 202 26 HETNAM 1EK {[5-(3-CHLORO-1-BENZOTHIOPHEN-2-YL)-4-PHENYL-4H-1,2,4- HETNAM 2 1EK TRIAZOL-3-YL]SULFANYL}ACETIC ACID FORMUL 2 1EK 2(C18 H12 CL N3 O2 S2) FORMUL 4 HOH *58(H2 O) HELIX 1 1 HIS A 0 LEU A 5 5 6 HELIX 2 2 GLY A 8 LYS A 16 1 9 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 LEU A 96 N MET A 57 SHEET 4 A 7 VAL A 76 THR A 86 -1 N ASN A 85 O VAL A 93 SHEET 5 A 7 ILE A 24 ILE A 33 -1 N LEU A 25 O CYS A 77 SHEET 6 A 7 ARG A 41 SER A 47 -1 O LEU A 45 N ILE A 28 SHEET 7 A 7 ASN A 51 LEU A 58 -1 O PHE A 56 N LEU A 44 SITE 1 AC1 10 ARG A 7 ARG A 41 ALA A 59 THR A 60 SITE 2 AC1 10 ASN A 85 1EK A 202 HOH A 306 HOH A 318 SITE 3 AC1 10 HOH A 339 HOH A 349 SITE 1 AC2 8 ARG A 31 ARG A 43 SER A 55 MET A 57 SITE 2 AC2 8 VAL A 93 1EK A 201 HOH A 341 HOH A 355 CRYST1 37.551 53.569 54.259 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 0.026630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018668 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018430 0.00000