HEADER TRANSCRIPTION/ANTITUMOR PROTEIN 15-NOV-14 2MWO TITLE SOLUTION STRUCTURE OF 53BP1 TANDEM TUDOR DOMAINS IN COMPLEX WITH A TITLE 2 P53K370ME2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUDOR-LIKE REGION RESIDUES 1484-1603; COMPND 5 SYNONYM: 53BP1, P53-BINDING PROTEIN 1, P53BP1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: DNA-BINDING REPRESSION REGION RESIDUES 363-377; COMPND 11 SYNONYM: P53K370ME2, ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR COMPND 12 SUPPRESSOR P53; COMPND 13 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: TP53BP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PTEV; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS CELL CYCLE, DNA DAMAGE RESPONSE, TRANSCRIPTION-ANTITUMOR PROTEIN KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,M.V.BOTUYAN,G.MER REVDAT 3 18-MAR-15 2MWO 1 JRNL REVDAT 2 21-JAN-15 2MWO 1 JRNL REVDAT 1 10-DEC-14 2MWO 0 JRNL AUTH Q.TONG,G.CUI,M.V.BOTUYAN,S.B.ROTHBART,R.HAYASHI, JRNL AUTH 2 C.A.MUSSELMAN,N.SINGH,E.APPELLA,B.D.STRAHL,G.MER, JRNL AUTH 3 T.G.KUTATELADZE JRNL TITL STRUCTURAL PLASTICITY OF METHYLLYSINE RECOGNITION BY THE JRNL TITL 2 TANDEM TUDOR DOMAIN OF 53BP1. JRNL REF STRUCTURE V. 23 312 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25579814 JRNL DOI 10.1016/J.STR.2014.11.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-14. REMARK 100 THE RCSB ID CODE IS RCSB104137. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 25 MM SODIUM PHOSPHATE, 1.5 MM REMARK 210 SODIUM AZIDE, 2.0 MM [U-100% 13C; REMARK 210 U-100% 15N] 53BP1-TUDOR, 6.0 MM REMARK 210 P53K370ME2, 90% H2O/10% D2O; 25 REMARK 210 MM SODIUM PHOSPHATE, 1.5 MM REMARK 210 SODIUM AZIDE, 2.0 MM [U-100% 13C; REMARK 210 U-100% 15N] 53BP1-TUDOR, 6.0 MM REMARK 210 P53K370ME2, 100% D2O; 25 MM REMARK 210 SODIUM PHOSPHATE, 1.5 MM SODIUM REMARK 210 AZIDE, 5.0 MM 53BP1-TUDOR, 2.0 MM REMARK 210 [U-100% 13C; U-100% 15N] REMARK 210 P53KC370ME2, 90% H2O/10% D2O; 25 REMARK 210 MM SODIUM PHOSPHATE, 1.5 MM REMARK 210 SODIUM AZIDE, 5.0 MM 53BP1-TUDOR, REMARK 210 2.0 MM [U-100% 13C; U-100% 15N] REMARK 210 P53KC370ME2, 100% D2O; 25 MM REMARK 210 SODIUM PHOSPHATE, 1.5 MM SODIUM REMARK 210 AZIDE, 2.0 MM [U-100% 15N] 53BP1- REMARK 210 TUDOR, 6.0 MM P53K370ME2, 90% REMARK 210 H2O/10% D2O; 35 MM SODIUM REMARK 210 PHOSPHATE, 1.5 MM SODIUM AZIDE, REMARK 210 2.0 MM P53K370ME2, 100% D2O; 25 REMARK 210 MM SODIUM PHOSPHATE, 1.5 MM REMARK 210 SODIUM AZIDE, 2.0 MM [U-100% 13C; REMARK 210 U-100% 15N] P53KC370ME2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D HNCA; REMARK 210 3D HNCACB; 3D HNCO; 3D CBCA(CO) REMARK 210 NH; 3D HN(CA)CO; 3D H(CCO)NH; 3D REMARK 210 C(CO)NH; 3D HBHA(CO)NH; 3D (H)CCH REMARK 210 -TOCSY; 3D 1H-15N TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D 1H-15N NOESY; REMARK 210 3D FILTERED (15N/13C)-EDITED REMARK 210 (13C); 3D (HB)CB(CGCD)HD REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE, NMRVIEW, SANE, REMARK 210 TALOS, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 OD1 ASP A 1550 HG SER B 366 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 4 TYR A1500 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 CYS A1535 CB - CA - C ANGL. DEV. = 7.7 DEGREES REMARK 500 13 ARG A1578 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 CYS A1535 CB - CA - C ANGL. DEV. = 7.9 DEGREES REMARK 500 17 CYS A1535 CB - CA - C ANGL. DEV. = 7.5 DEGREES REMARK 500 19 CYS A1535 CB - CA - C ANGL. DEV. = 7.6 DEGREES 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 1 HIS A -2 -47.00 -151.64 REMARK 500 1 SER A1485 92.35 -66.20 REMARK 500 1 PHE A1486 -64.71 69.37 REMARK 500 1 SER A1496 -175.02 -65.31 REMARK 500 1 ALA A1512 9.29 56.88 REMARK 500 1 ASP A1536 55.47 -115.48 REMARK 500 1 ASP A1541 -3.60 74.64 REMARK 500 1 GLU A1551 -20.03 155.55 REMARK 500 1 HIS B 368 -129.07 49.19 REMARK 500 1 SER B 376 69.54 34.63 REMARK 500 2 SER A1485 99.55 -64.35 REMARK 500 2 PHE A1486 -66.08 66.91 REMARK 500 2 ALA A1512 9.30 57.25 REMARK 500 2 ASP A1536 63.09 -118.51 REMARK 500 2 ASP A1541 -2.93 72.36 REMARK 500 2 GLU A1551 -14.48 55.15 REMARK 500 2 SER B 366 46.09 -73.80 REMARK 500 2 SER B 367 -28.02 69.81 REMARK 500 2 HIS B 368 -154.64 48.70 REMARK 500 2 GLN B 375 -7.80 -152.45 REMARK 500 3 SER A1485 99.90 -63.29 REMARK 500 3 PHE A1486 -64.24 67.04 REMARK 500 3 ALA A1512 8.79 58.87 REMARK 500 3 ASP A1536 62.78 -118.55 REMARK 500 3 ASP A1541 -2.14 71.65 REMARK 500 3 GLU A1551 8.44 -52.48 REMARK 500 3 SER B 366 173.82 -59.26 REMARK 500 3 HIS B 368 -92.88 48.53 REMARK 500 3 LYS B 372 -62.59 -128.97 REMARK 500 3 GLN B 375 -43.80 -140.85 REMARK 500 4 SER A1485 86.91 -65.54 REMARK 500 4 PHE A1486 -65.03 69.29 REMARK 500 4 SER A1496 -172.26 -65.74 REMARK 500 4 ASP A1536 57.58 -118.45 REMARK 500 4 ASP A1541 -4.60 74.20 REMARK 500 4 GLU A1551 -25.82 -179.92 REMARK 500 4 HIS B 368 -111.35 45.90 REMARK 500 4 SER B 371 -55.13 -24.71 REMARK 500 5 SER A1485 95.42 -64.59 REMARK 500 5 PHE A1486 -65.10 67.00 REMARK 500 5 SER A1497 45.26 -76.76 REMARK 500 5 ALA A1512 10.70 56.74 REMARK 500 5 ASP A1536 65.01 -115.78 REMARK 500 5 ASP A1541 -3.60 74.14 REMARK 500 5 GLU A1549 15.32 -67.92 REMARK 500 5 ASP A1550 -57.47 -123.49 REMARK 500 5 GLU A1551 -21.51 -167.17 REMARK 500 5 HIS B 368 -96.77 49.79 REMARK 500 6 SER A1485 85.95 -67.73 REMARK 500 6 PHE A1486 -62.06 69.45 REMARK 500 REMARK 500 THIS ENTRY HAS 198 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 10 GLU A1551 24.9 L L OUTSIDE RANGE REMARK 500 11 GLU A1551 24.9 L L OUTSIDE RANGE 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 MLY B 370 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25347 RELATED DB: BMRB REMARK 900 RELATED ID: 2MWP RELATED DB: PDB DBREF 2MWO A 1484 1603 UNP Q12888 TP53B_HUMAN 1484 1603 DBREF 2MWO B 363 377 UNP P04637 P53_HUMAN 363 377 SEQADV 2MWO GLY A -3 UNP Q12888 EXPRESSION TAG SEQADV 2MWO HIS A -2 UNP Q12888 EXPRESSION TAG SEQADV 2MWO MET A -1 UNP Q12888 EXPRESSION TAG SEQRES 1 A 123 GLY HIS MET ASN SER PHE VAL GLY LEU ARG VAL VAL ALA SEQRES 2 A 123 LYS TRP SER SER ASN GLY TYR PHE TYR SER GLY LYS ILE SEQRES 3 A 123 THR ARG ASP VAL GLY ALA GLY LYS TYR LYS LEU LEU PHE SEQRES 4 A 123 ASP ASP GLY TYR GLU CYS ASP VAL LEU GLY LYS ASP ILE SEQRES 5 A 123 LEU LEU CYS ASP PRO ILE PRO LEU ASP THR GLU VAL THR SEQRES 6 A 123 ALA LEU SER GLU ASP GLU TYR PHE SER ALA GLY VAL VAL SEQRES 7 A 123 LYS GLY HIS ARG LYS GLU SER GLY GLU LEU TYR TYR SER SEQRES 8 A 123 ILE GLU LYS GLU GLY GLN ARG LYS TRP TYR LYS ARG MET SEQRES 9 A 123 ALA VAL ILE LEU SER LEU GLU GLN GLY ASN ARG LEU ARG SEQRES 10 A 123 GLU GLN TYR GLY LEU GLY SEQRES 1 B 15 ARG ALA HIS SER SER HIS LEU MLY SER LYS LYS GLY GLN SEQRES 2 B 15 SER THR MODRES 2MWO MLY B 370 LYS N-DIMETHYL-LYSINE HET MLY B 370 28 HETNAM MLY N-DIMETHYL-LYSINE FORMUL 2 MLY C8 H18 N2 O2 HELIX 1 1 SER A 1589 GLY A 1601 1 13 SHEET 1 A 5 GLU A1524 LEU A1528 0 SHEET 2 A 5 LYS A1514 PHE A1519 -1 N TYR A1515 O VAL A1527 SHEET 3 A 5 PHE A1501 GLY A1511 -1 N ARG A1508 O LYS A1516 SHEET 4 A 5 ARG A1490 LYS A1494 -1 N VAL A1491 O GLY A1504 SHEET 5 A 5 ILE A1532 LEU A1533 -1 O LEU A1533 N VAL A1492 SHEET 1 B 5 GLN A1577 LYS A1582 0 SHEET 2 B 5 GLU A1567 LYS A1574 -1 N ILE A1572 O LYS A1579 SHEET 3 B 5 PHE A1553 GLU A1564 -1 N LYS A1559 O SER A1571 SHEET 4 B 5 GLU A1543 LEU A1547 -1 N VAL A1544 O GLY A1556 SHEET 5 B 5 VAL A1586 ILE A1587 -1 O ILE A1587 N THR A1545 LINK C LEU B 369 N MLY B 370 1555 1555 1.33 LINK C MLY B 370 N SER B 371 1555 1555 1.33 SITE 1 AC1 9 TRP A1495 TYR A1502 ASP A1521 TYR A1523 SITE 2 AC1 9 LEU B 369 SER B 371 LYS B 372 LYS B 373 SITE 3 AC1 9 GLN B 375 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1