HEADER PEPTIDE BINDING PROTEIN 31-OCT-11 3UEN TITLE CRYSTAL STRUCTURE OF TOPBP1 BRCT4/5 DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 2-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BRCT DOMAIN; COMPND 5 SYNONYM: DNA TOPOISOMERASE II-BETA-BINDING PROTEIN 1, TOPBP1, DNA COMPND 6 TOPOISOMERASE II-BINDING PROTEIN 1; COMPND 7 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: KIAA0259, TOPBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS BRCT DOMAIN, PHOSPHO-PEPTIDE BINDING, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.C.LEUNG,J.N.M.GLOVER REVDAT 4 28-FEB-24 3UEN 1 REMARK SEQADV REVDAT 3 08-NOV-17 3UEN 1 REMARK REVDAT 2 26-MAR-14 3UEN 1 JRNL REVDAT 1 03-JUL-13 3UEN 0 JRNL AUTH C.C.LEUNG,L.SUN,Z.GONG,M.BURKAT,R.EDWARDS,M.ASSMUS,J.CHEN, JRNL AUTH 2 J.N.GLOVER JRNL TITL STRUCTURAL INSIGHTS INTO RECOGNITION OF MDC1 BY TOPBP1 IN JRNL TITL 2 DNA REPLICATION CHECKPOINT CONTROL. JRNL REF STRUCTURE V. 21 1450 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23891287 JRNL DOI 10.1016/J.STR.2013.06.015 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 927 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 38.5982 - 3.6337 0.99 2607 140 0.1761 0.2084 REMARK 3 2 3.6337 - 2.8845 1.00 2496 127 0.1547 0.2245 REMARK 3 3 2.8845 - 2.5200 1.00 2466 127 0.1736 0.2097 REMARK 3 4 2.5200 - 2.2896 1.00 2443 131 0.1754 0.2246 REMARK 3 5 2.2896 - 2.1255 1.00 2395 127 0.1810 0.2387 REMARK 3 6 2.1255 - 2.0002 1.00 2427 133 0.1814 0.2424 REMARK 3 7 2.0002 - 1.9000 0.99 2376 142 0.2302 0.2807 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 25.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.950 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) : 17.58520 REMARK 3 B22 (A**2) : 9.56310 REMARK 3 B33 (A**2) : 6.01250 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 1603 REMARK 3 ANGLE : 1.347 2174 REMARK 3 CHIRALITY : 0.085 252 REMARK 3 PLANARITY : 0.005 274 REMARK 3 DIHEDRAL : 14.537 597 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -0.4566 49.5704 76.5804 REMARK 3 T TENSOR REMARK 3 T11: 0.0137 T22: 0.0113 REMARK 3 T33: 0.0078 T12: 0.0141 REMARK 3 T13: 0.0119 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 0.1582 L22: 0.4039 REMARK 3 L33: 0.3347 L12: 0.0587 REMARK 3 L13: 0.0020 L23: -0.1843 REMARK 3 S TENSOR REMARK 3 S11: 0.0131 S12: 0.0302 S13: 0.0333 REMARK 3 S21: -0.0343 S22: -0.0198 S23: -0.0287 REMARK 3 S31: -0.0395 S32: 0.0233 S33: 0.0076 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 3UEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11588 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18140 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 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 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NASCN, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.04400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.04400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1093 LIES ON A SPECIAL POSITION. 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 544 REMARK 465 PRO A 545 REMARK 465 LEU A 546 REMARK 465 GLY A 547 REMARK 465 SER A 548 REMARK 465 GLU A 549 REMARK 465 GLU A 745 REMARK 465 ARG A 746 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 933 O HOH A 1021 2.18 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 SCN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 806 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UEO RELATED DB: PDB DBREF 3UEN A 549 746 UNP Q92547 TOPB1_HUMAN 549 746 SEQADV 3UEN GLY A 544 UNP Q92547 EXPRESSION TAG SEQADV 3UEN PRO A 545 UNP Q92547 EXPRESSION TAG SEQADV 3UEN LEU A 546 UNP Q92547 EXPRESSION TAG SEQADV 3UEN GLY A 547 UNP Q92547 EXPRESSION TAG SEQADV 3UEN SER A 548 UNP Q92547 EXPRESSION TAG SEQRES 1 A 203 GLY PRO LEU GLY SER GLU GLU GLY LEU PHE SER GLN LYS SEQRES 2 A 203 SER PHE LEU VAL LEU GLY PHE SER ASN GLU ASN GLU SER SEQRES 3 A 203 ASN ILE ALA ASN ILE ILE LYS GLU ASN ALA GLY LYS ILE SEQRES 4 A 203 MET SER LEU LEU SER ARG THR VAL ALA ASP TYR ALA VAL SEQRES 5 A 203 VAL PRO LEU LEU GLY CYS GLU VAL GLU ALA THR VAL GLY SEQRES 6 A 203 GLU VAL VAL THR ASN THR TRP LEU VAL THR CYS ILE ASP SEQRES 7 A 203 TYR GLN THR LEU PHE ASP PRO LYS SER ASN PRO LEU PHE SEQRES 8 A 203 THR PRO VAL PRO VAL MET THR GLY MET THR PRO LEU GLU SEQRES 9 A 203 ASP CYS VAL ILE SER PHE SER GLN CYS ALA GLY ALA GLU SEQRES 10 A 203 LYS GLU SER LEU THR PHE LEU ALA ASN LEU LEU GLY ALA SEQRES 11 A 203 SER VAL GLN GLU TYR PHE VAL ARG LYS SER ASN ALA LYS SEQRES 12 A 203 LYS GLY MET PHE ALA SER THR HIS LEU ILE LEU LYS GLU SEQRES 13 A 203 ARG GLY GLY SER LYS TYR GLU ALA ALA LYS LYS TRP ASN SEQRES 14 A 203 LEU PRO ALA VAL THR ILE ALA TRP LEU LEU GLU THR ALA SEQRES 15 A 203 ARG THR GLY LYS ARG ALA ASP GLU SER HIS PHE LEU ILE SEQRES 16 A 203 GLU ASN SER THR LYS GLU GLU ARG HET SCN A 801 3 HET GOL A 802 6 HET GOL A 803 6 HET GOL A 804 6 HET GOL A 805 6 HET GOL A 806 6 HETNAM SCN THIOCYANATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SCN C N S 1- FORMUL 3 GOL 5(C3 H8 O3) FORMUL 8 HOH *238(H2 O) HELIX 1 1 ASN A 565 GLU A 577 1 13 HELIX 2 2 ASN A 613 ASP A 621 1 9 HELIX 3 3 PRO A 628 SER A 630 1 3 HELIX 4 4 PRO A 632 PHE A 634 1 3 HELIX 5 5 GLY A 658 LEU A 670 1 13 HELIX 6 6 SER A 703 LYS A 710 1 8 HELIX 7 7 ILE A 718 THR A 727 1 10 HELIX 8 8 GLU A 733 HIS A 735 1 3 HELIX 9 9 ILE A 738 ASN A 740 1 3 SHEET 1 A 4 LYS A 581 ILE A 582 0 SHEET 2 A 4 SER A 557 VAL A 560 1 N PHE A 558 O LYS A 581 SHEET 3 A 4 ALA A 591 VAL A 596 1 O VAL A 595 N LEU A 559 SHEET 4 A 4 VAL A 607 THR A 612 1 O VAL A 611 N ALA A 594 SHEET 1 B 4 SER A 674 VAL A 675 0 SHEET 2 B 4 VAL A 650 PHE A 653 1 N ILE A 651 O SER A 674 SHEET 3 B 4 HIS A 694 ILE A 696 1 O ILE A 696 N SER A 652 SHEET 4 B 4 ALA A 715 VAL A 716 1 O VAL A 716 N LEU A 695 SITE 1 AC1 3 THR A 612 ASN A 613 THR A 614 SITE 1 AC2 7 LEU A 559 VAL A 560 GLU A 568 ILE A 582 SITE 2 AC2 7 MET A 583 SER A 584 HOH A1108 SITE 1 AC3 5 VAL A 639 MET A 640 ARG A 726 HOH A 953 SITE 2 AC3 5 HOH A1057 SITE 1 AC4 7 CYS A 601 VAL A 603 LEU A 722 GLU A 723 SITE 2 AC4 7 ARG A 726 HOH A1003 HOH A1115 SITE 1 AC5 6 ASN A 567 ASN A 570 ILE A 574 ASN A 613 SITE 2 AC5 6 VAL A 617 HOH A1028 SITE 1 AC6 6 ASN A 565 GLU A 568 SER A 569 SER A 734 SITE 2 AC6 6 HIS A 735 HOH A1125 CRYST1 35.902 48.801 126.088 90.00 90.00 90.00 P 2 2 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 0.027854 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007931 0.00000