HEADER TRANSCRIPTION/ANTITUMOR PROTEIN 15-NOV-14 2MWP TITLE SOLUTION STRUCTURE OF 53BP1 TANDEM TUDOR DOMAINS IN COMPLEX WITH A TITLE 2 P53K382ME2 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 376-387; COMPND 11 SYNONYM: P53K382ME2, 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 2MWP 1 JRNL REVDAT 2 21-JAN-15 2MWP 1 JRNL REVDAT 1 10-DEC-14 2MWP 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 2MWP 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 RCSB104138. 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 P53K382ME2, 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 P53K382ME2, 100% D2O; 25 MM REMARK 210 SODIUM PHOSPHATE, 1.5 MM SODIUM REMARK 210 AZIDE, 2.0 MM 53BP1-TUDOR, 0.5 MM REMARK 210 [U-100% 13C; U-100% 15N] REMARK 210 P53KC382ME2, 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 P53K382ME2, 90% REMARK 210 H2O/10% D2O; 25 MM SODIUM REMARK 210 PHOSPHATE, 1.5 MM SODIUM AZIDE, REMARK 210 2.0 MM P53K382ME2, 100% D2O; 25 REMARK 210 MM SODIUM PHOSPHATE, 1.5 MM REMARK 210 SODIUM AZIDE, 0.5 MM [U-100% 13C; REMARK 210 U-100% 15N] P53KC382ME2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HBHA(CO)NH; 3D C(CO)NH; 3D REMARK 210 H(CCO)NH; 3D (H)CCH-TOCSY; 3D 1H- REMARK 210 15N TOCSY; 2D (HB)CB(CGCD)HD; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D FILTERED(13C/15N)- REMARK 210 EDITED (13C) 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, AMBER, PROCHECKNMR 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: 548 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1807 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.6 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 HG SER A 1503 OD2 ASP A 1520 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 1 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 TYR A1500 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 ARG A1597 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 TYR A1500 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A1583 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG B 379 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 5 TYR A1500 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 6 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG A1578 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 7 ARG A1595 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG B 379 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG B 379 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 12 ARG A1595 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A1508 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A1595 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A1583 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A1597 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 ARG B 379 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 15 ARG A1583 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A1595 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A1595 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 16 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 TYR A1500 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 17 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 18 TYR A1500 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 ARG A1595 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG A1578 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 19 ARG A1583 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG B 379 NE - CZ - NH1 ANGL. DEV. = 4.0 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 SER A1485 61.46 -66.48 REMARK 500 1 PHE A1486 -56.70 69.90 REMARK 500 1 VAL A1487 97.84 -49.84 REMARK 500 1 SER A1497 48.83 -76.57 REMARK 500 1 ALA A1512 4.39 57.33 REMARK 500 1 ASP A1536 58.68 -119.54 REMARK 500 1 GLU A1551 -4.97 79.79 REMARK 500 1 SER A1565 -37.13 58.03 REMARK 500 1 LYS B 381 -67.31 -10.13 REMARK 500 2 SER A1485 64.42 -62.49 REMARK 500 2 PHE A1486 -53.13 67.14 REMARK 500 2 SER A1496 -177.78 -65.46 REMARK 500 2 ARG A1508 136.49 -170.50 REMARK 500 2 ALA A1512 4.16 56.81 REMARK 500 2 ASP A1536 62.90 -117.08 REMARK 500 2 ASP A1541 -0.52 67.79 REMARK 500 2 GLU A1551 -14.72 88.29 REMARK 500 2 MET B 384 142.24 -171.32 REMARK 500 3 PHE A1486 -54.69 -156.76 REMARK 500 3 VAL A1487 99.47 -47.92 REMARK 500 3 ASN A1498 15.59 -166.46 REMARK 500 3 TYR A1500 -168.85 -105.28 REMARK 500 3 ARG A1508 136.79 -172.17 REMARK 500 3 ALA A1512 4.86 57.13 REMARK 500 3 ASP A1536 58.40 -111.59 REMARK 500 3 SER A1565 28.35 45.10 REMARK 500 3 MLY B 382 -31.91 -140.73 REMARK 500 4 SER A1485 -83.77 12.73 REMARK 500 4 PHE A1486 -43.95 -143.78 REMARK 500 4 SER A1497 47.94 -75.24 REMARK 500 4 ARG A1508 137.73 -172.25 REMARK 500 4 ALA A1512 5.31 56.58 REMARK 500 4 ASP A1536 63.15 -118.35 REMARK 500 4 GLU A1551 -14.78 96.50 REMARK 500 4 MLY B 382 -11.06 45.58 REMARK 500 4 MET B 384 120.42 179.93 REMARK 500 5 SER A1485 56.28 -69.90 REMARK 500 5 PHE A1486 -48.45 70.32 REMARK 500 5 VAL A1487 98.76 -68.05 REMARK 500 5 SER A1497 42.33 -73.10 REMARK 500 5 ARG A1508 136.42 -171.95 REMARK 500 5 ALA A1512 3.28 57.17 REMARK 500 5 ASP A1536 58.69 -112.30 REMARK 500 5 ASP A1541 -0.15 69.35 REMARK 500 5 GLU A1551 -13.19 86.92 REMARK 500 5 SER A1565 -42.78 58.39 REMARK 500 5 ARG A1595 -0.91 -58.55 REMARK 500 5 LEU B 383 12.59 116.22 REMARK 500 6 SER A1485 171.12 -55.57 REMARK 500 6 PHE A1486 -51.19 -25.90 REMARK 500 REMARK 500 THIS ENTRY HAS 197 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25348 RELATED DB: BMRB REMARK 900 RELATED ID: 2MWO RELATED DB: PDB DBREF 2MWP A 1484 1603 UNP Q12888 TP53B_HUMAN 1484 1603 DBREF 2MWP B 376 387 UNP P04637 P53_HUMAN 376 387 SEQADV 2MWP GLY A -3 UNP Q12888 EXPRESSION TAG SEQADV 2MWP HIS A -2 UNP Q12888 EXPRESSION TAG SEQADV 2MWP 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 12 SER THR SER ARG HIS LYS MLY LEU MET PHE LYS THR MODRES 2MWP MLY B 382 LYS N-DIMETHYL-LYSINE HET MLY B 382 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 THR A1507 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 VAL A1557 O GLU A1573 SHEET 4 B 5 GLU A1543 LEU A1547 -1 N ALA A1546 O SER A1554 SHEET 5 B 5 VAL A1586 ILE A1587 -1 O ILE A1587 N THR A1545 LINK C LYS B 381 N MLY B 382 1555 1555 1.34 LINK C MLY B 382 N LEU B 383 1555 1555 1.34 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