HEADER PROTEIN BINDING 09-JAN-13 4IPD TITLE STRUCTURE OF THE N-TERMINAL DOMAIN OF RPA70, E100R MUTANT 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 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 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.D.FELDKAMP,A.O.FRANK,B.VANGAMUDI,S.W.FESIK,W.J.CHAZIN REVDAT 3 20-SEP-23 4IPD 1 SEQADV REVDAT 2 02-OCT-13 4IPD 1 JRNL REVDAT 1 11-SEP-13 4IPD 0 JRNL AUTH M.D.FELDKAMP,A.O.FRANK,J.P.KENNEDY,J.D.PATRONE,B.VANGAMUDI, JRNL AUTH 2 A.G.WATERSON,S.W.FESIK,W.J.CHAZIN JRNL TITL SURFACE REENGINEERING OF RPA70N ENABLES COCRYSTALLIZATION JRNL TITL 2 WITH AN INHIBITOR OF THE REPLICATION PROTEIN A INTERACTION JRNL TITL 3 MOTIF OF ATR INTERACTING PROTEIN. JRNL REF BIOCHEMISTRY V. 52 6515 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23962067 JRNL DOI 10.1021/BI400542Z REMARK 2 REMARK 2 RESOLUTION. 1.51 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 843 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 36.0630 - 2.7426 1.00 2785 141 0.1428 0.1822 REMARK 3 2 2.7426 - 2.1770 1.00 2642 141 0.1374 0.1358 REMARK 3 3 2.1770 - 1.9018 1.00 2654 132 0.1212 0.1556 REMARK 3 4 1.9018 - 1.7279 1.00 2599 138 0.1333 0.1687 REMARK 3 5 1.7279 - 1.6041 1.00 2596 148 0.1379 0.1779 REMARK 3 6 1.6041 - 1.5095 0.96 2499 143 0.1408 0.1863 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.40 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.70 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 : 0.007 1054 REMARK 3 ANGLE : 1.295 1442 REMARK 3 CHIRALITY : 0.071 171 REMARK 3 PLANARITY : 0.006 192 REMARK 3 DIHEDRAL : 13.037 423 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): 2.1933 1.3899 4.8299 REMARK 3 T TENSOR REMARK 3 T11: 0.0273 T22: 0.0427 REMARK 3 T33: 0.0460 T12: 0.0039 REMARK 3 T13: 0.0050 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.7373 L22: 0.8490 REMARK 3 L33: 0.7205 L12: 0.1463 REMARK 3 L13: 0.0097 L23: -0.0934 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: 0.0165 S13: -0.0332 REMARK 3 S21: -0.0012 S22: -0.0142 S23: -0.0062 REMARK 3 S31: 0.0312 S32: 0.0307 S33: -0.0061 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 4IPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 36.053 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.510 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 40.3800 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: PHENIX 1.8.1_1168 REMARK 200 STARTING MODEL: 2B29 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, 2M AMMONIUM SULFATE, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 19.71250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.93350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.07450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.93350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.71250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.07450 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: 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 SG CYS A 75 O HOH A 236 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN A 70 O HOH A 279 4455 2.02 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 20 48.37 -94.60 REMARK 500 ASN A 74 -14.44 93.96 REMARK 500 ASN A 74 -12.12 93.96 REMARK 500 VAL A 108 -61.18 -98.42 REMARK 500 ASN A 119 58.94 -152.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IPC RELATED DB: PDB REMARK 900 RELATED ID: 4IPG RELATED DB: PDB REMARK 900 RELATED ID: 4IPH RELATED DB: PDB DBREF 4IPD A 1 120 UNP P27694 RFA1_HUMAN 1 120 SEQADV 4IPD GLY A -2 UNP P27694 EXPRESSION TAG SEQADV 4IPD SER A -1 UNP P27694 EXPRESSION TAG SEQADV 4IPD HIS A 0 UNP P27694 EXPRESSION TAG SEQADV 4IPD ARG A 100 UNP P27694 GLU 100 ENGINEERED MUTATION SEQRES 1 A 123 GLY SER HIS MET VAL GLY GLN LEU SER GLU 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 ARG 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 FORMUL 2 HOH *156(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 ILE A 83 O ILE A 95 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 ARG A 43 N ARG A 31 SHEET 7 A 7 ASN A 51 LEU A 58 -1 O PHE A 56 N LEU A 44 CRYST1 39.425 50.149 51.867 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 0.025365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019280 0.00000