HEADER PROTEIN BINDING 29-MAR-16 5J26 TITLE CRYSTAL STRUCTURE OF A 53BP1 TUDOR DOMAIN IN COMPLEX WITH A UBIQUITIN TITLE 2 VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN VARIANT I53; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: P53BP1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: TP53BP1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TUDOR DOMAIN UBIQUITIN VARIANT, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.WAN,M.CANNY,Y.C.JUANG,D.DUROCHER,F.SICHERI REVDAT 4 06-MAR-24 5J26 1 REMARK REVDAT 3 27-SEP-17 5J26 1 REMARK REVDAT 2 21-DEC-16 5J26 1 REMARK REVDAT 1 14-DEC-16 5J26 0 JRNL AUTH L.WAN,M.CANNY,Y.C.JUANG,D.DUROCHER,F.SICHERI JRNL TITL A GENETICALLY ENCODED INHIBITOR OF 53BP1 TO STIMULATE JRNL TITL 2 HOMOLOGY-BASED GENE EDITING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.367 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 6047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.005 REMARK 3 FREE R VALUE TEST SET COUNT : 605 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 24.5944 - 3.9718 0.99 1528 170 0.1962 0.2370 REMARK 3 2 3.9718 - 3.1547 1.00 1468 163 0.2316 0.2939 REMARK 3 3 3.1547 - 2.7565 0.98 1419 158 0.2852 0.3899 REMARK 3 4 2.7565 - 2.5047 0.72 1027 114 0.2939 0.3195 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.886 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.57 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 : 0.002 1540 REMARK 3 ANGLE : 0.701 2071 REMARK 3 CHIRALITY : 0.023 231 REMARK 3 PLANARITY : 0.002 263 REMARK 3 DIHEDRAL : 12.279 593 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): -11.5312 -8.7604 11.5442 REMARK 3 T TENSOR REMARK 3 T11: 0.1727 T22: 0.3482 REMARK 3 T33: 0.2399 T12: 0.0061 REMARK 3 T13: 0.0085 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 1.7504 L22: 4.2620 REMARK 3 L33: 2.0927 L12: 0.4637 REMARK 3 L13: -0.3965 L23: -0.7731 REMARK 3 S TENSOR REMARK 3 S11: 0.0580 S12: -0.5397 S13: 0.1017 REMARK 3 S21: 0.1970 S22: -0.0142 S23: 0.0539 REMARK 3 S31: -0.0042 S32: -0.0109 S33: -0.0508 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 5J26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 93.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6047 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 24.593 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 200 DATA REDUNDANCY : 1.750 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.16 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.750 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.0, 0.2 M REMARK 280 SODIUM ACETATE, 27% (W/V) PEG8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K 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 19.76550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.11850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.88400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.11850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.76550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.88400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 1511 REMARK 465 ALA A 1512 REMARK 465 GLY A 1513 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A1523 CG CD1 CD2 CE1 CE2 CZ OH 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 LYS B 63 -115.68 -127.32 REMARK 500 LEU A1534 76.40 -100.73 REMARK 500 GLU A1551 34.91 70.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 5J26 B 0 75 PDB 5J26 5J26 0 75 DBREF 5J26 A 1487 1603 UNP Q12888 TP53B_HUMAN 1492 1608 SEQRES 1 B 76 ALA MET LEU ILE PHE VAL LYS THR LEU THR GLY LYS THR SEQRES 2 B 76 ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN SEQRES 3 B 76 VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO SEQRES 4 B 76 ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS SER LEU GLU SEQRES 5 B 76 ASP GLY ARG THR LEU SER ASP TYR ASN ILE LEU LYS ASP SEQRES 6 B 76 SER LYS LEU HIS PRO LEU LEU ARG LEU ARG GLY SEQRES 1 A 117 VAL GLY LEU ARG VAL VAL ALA LYS TRP SER SER ASN GLY SEQRES 2 A 117 TYR PHE TYR SER GLY LYS ILE THR ARG ASP VAL GLY ALA SEQRES 3 A 117 GLY LYS TYR LYS LEU LEU PHE ASP ASP GLY TYR GLU CYS SEQRES 4 A 117 ASP VAL LEU GLY LYS ASP ILE LEU LEU CYS ASP PRO ILE SEQRES 5 A 117 PRO LEU ASP THR GLU VAL THR ALA LEU SER GLU ASP GLU SEQRES 6 A 117 TYR PHE SER ALA GLY VAL VAL LYS GLY HIS ARG LYS GLU SEQRES 7 A 117 SER GLY GLU LEU TYR TYR SER ILE GLU LYS GLU GLY GLN SEQRES 8 A 117 ARG LYS TRP TYR LYS ARG MET ALA VAL ILE LEU SER LEU SEQRES 9 A 117 GLU GLN GLY ASN ARG LEU ARG GLU GLN TYR GLY LEU GLY FORMUL 3 HOH *(H2 O) HELIX 1 AA1 THR B 22 GLY B 35 1 14 HELIX 2 AA2 PRO B 37 GLN B 41 5 5 HELIX 3 AA3 THR B 55 ASN B 60 5 6 HELIX 4 AA4 LEU A 1528 LYS A 1530 5 3 HELIX 5 AA5 SER A 1589 ARG A 1595 1 7 HELIX 6 AA6 LEU A 1596 GLY A 1601 1 6 SHEET 1 AA1 6 THR B 12 VAL B 17 0 SHEET 2 AA1 6 MET B 1 LYS B 6 -1 N MET B 1 O VAL B 17 SHEET 3 AA1 6 HIS B 68 LEU B 73 1 O LEU B 71 N PHE B 4 SHEET 4 AA1 6 TYR A1552 LYS A1563 -1 O PHE A1553 N HIS B 68 SHEET 5 AA1 6 LEU A1568 LYS A1574 -1 O SER A1571 N GLY A1560 SHEET 6 AA1 6 GLN A1577 LYS A1582 -1 O GLN A1577 N LYS A1574 SHEET 1 AA2 6 LYS B 48 LEU B 50 0 SHEET 2 AA2 6 LEU B 43 PHE B 45 -1 N LEU B 43 O LEU B 50 SHEET 3 AA2 6 HIS B 68 LEU B 73 -1 O ARG B 72 N ILE B 44 SHEET 4 AA2 6 TYR A1552 LYS A1563 -1 O PHE A1553 N HIS B 68 SHEET 5 AA2 6 GLU A1543 LEU A1547 -1 N ALA A1546 O SER A1554 SHEET 6 AA2 6 VAL A1586 ILE A1587 -1 O ILE A1587 N THR A1545 SHEET 1 AA3 5 GLU A1524 VAL A1527 0 SHEET 2 AA3 5 TYR A1515 PHE A1519 -1 N TYR A1515 O VAL A1527 SHEET 3 AA3 5 TYR A1502 ARG A1508 -1 N ARG A1508 O LYS A1516 SHEET 4 AA3 5 ARG A1490 ALA A1493 -1 N ALA A1493 O TYR A1502 SHEET 5 AA3 5 ILE A1532 LEU A1533 -1 O LEU A1533 N VAL A1492 CRYST1 39.531 47.768 94.237 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 0.025297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010612 0.00000