HEADER RNA BINDING PROTEIN 18-FEB-16 5I7X TITLE BRD9 IN COMPLEX WITH CPD2 (N,N-DIMETHYL-3-(6-METHYL-7-OXO-6,7-DIHYDRO- TITLE 2 1H-PYRROLO[2,3-C]PYRIDIN-4-YL)BENZAMIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8; COMPND 5 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: BRD9, UNQ3040/PRO9856; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN INHIBITOR EPIGENETICS STRUCTURE-BASED DRUG DESIGN, RNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MURRAY REVDAT 2 06-MAR-24 5I7X 1 JRNL REMARK REVDAT 1 12-OCT-16 5I7X 0 JRNL AUTH T.D.CRAWFORD,V.TSUI,E.M.FLYNN,S.WANG,A.M.TAYLOR,A.COTE, JRNL AUTH 2 J.E.AUDIA,M.H.BERESINI,D.J.BURDICK,R.CUMMINGS,L.A.DAKIN, JRNL AUTH 3 M.DUPLESSIS,A.C.GOOD,M.C.HEWITT,H.R.HUANG,H.JAYARAM, JRNL AUTH 4 J.R.KIEFER,Y.JIANG,J.MURRAY,C.G.NASVESCHUK,E.PARDO,F.POY, JRNL AUTH 5 F.A.ROMERO,Y.TANG,J.WANG,Z.XU,L.E.ZAWADZKE,X.ZHU, JRNL AUTH 6 B.K.ALBRECHT,S.R.MAGNUSON,S.BELLON,A.G.COCHRAN JRNL TITL DIVING INTO THE WATER: INDUCIBLE BINDING CONFORMATIONS FOR JRNL TITL 2 BRD4, TAF1(2), BRD9, AND CECR2 BROMODOMAINS. JRNL REF J.MED.CHEM. V. 59 5391 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27219867 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00264 REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 3 NUMBER OF REFLECTIONS : 32236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1625 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 18.0689 - 2.6879 0.86 2557 112 0.1587 0.1626 REMARK 3 2 2.6879 - 2.1345 0.81 2389 140 0.1531 0.1656 REMARK 3 3 2.1345 - 1.8650 0.84 2467 140 0.1328 0.1482 REMARK 3 4 1.8650 - 1.6946 0.87 2562 137 0.1374 0.1579 REMARK 3 5 1.6946 - 1.5733 0.87 2607 132 0.1285 0.1551 REMARK 3 6 1.5733 - 1.4805 0.87 2560 133 0.1338 0.1836 REMARK 3 7 1.4805 - 1.4064 0.87 2604 132 0.1425 0.1768 REMARK 3 8 1.4064 - 1.3452 0.88 2602 124 0.1540 0.1654 REMARK 3 9 1.3452 - 1.2935 0.87 2543 157 0.1716 0.2106 REMARK 3 10 1.2935 - 1.2488 0.87 2573 147 0.1842 0.1792 REMARK 3 11 1.2488 - 1.2098 0.87 2591 141 0.1954 0.2144 REMARK 3 12 1.2098 - 1.1752 0.87 2556 130 0.2084 0.2149 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.87 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 : 0.003 877 REMARK 3 ANGLE : 0.669 1185 REMARK 3 CHIRALITY : 0.063 124 REMARK 3 PLANARITY : 0.006 151 REMARK 3 DIHEDRAL : 15.094 321 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5I7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.175 REMARK 200 RESOLUTION RANGE LOW (A) : 18.067 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40100 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, PH 6.5, 20% PEG 2000 REMARK 280 MONOMETHYLETHER, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 SER A 22 N REMARK 470 ARG A 38 CZ NH1 NH2 REMARK 470 ASP A 103 CG OD1 OD2 REMARK 470 SER A 122 OG 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 401 O HOH A 452 2.03 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 ASP A 103 57.52 -92.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 460 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 461 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 462 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 463 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 464 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 465 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 466 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 467 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH A 468 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH A 469 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A 470 DISTANCE = 7.43 ANGSTROMS REMARK 525 HOH A 471 DISTANCE = 7.62 ANGSTROMS REMARK 525 HOH A 472 DISTANCE = 7.82 ANGSTROMS REMARK 525 HOH A 473 DISTANCE = 8.45 ANGSTROMS REMARK 525 HOH A 474 DISTANCE = 8.51 ANGSTROMS REMARK 525 HOH A 475 DISTANCE = 8.55 ANGSTROMS REMARK 525 HOH A 476 DISTANCE = 8.76 ANGSTROMS REMARK 525 HOH A 477 DISTANCE = 8.77 ANGSTROMS REMARK 525 HOH A 478 DISTANCE = 8.85 ANGSTROMS REMARK 525 HOH A 479 DISTANCE = 9.14 ANGSTROMS REMARK 525 HOH A 480 DISTANCE = 9.51 ANGSTROMS REMARK 525 HOH A 481 DISTANCE = 9.66 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 67B A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5I40 RELATED DB: PDB DBREF 5I7X A 22 122 UNP Q9H8M2 BRD9_HUMAN 138 238 SEQRES 1 A 101 SER THR PRO ILE GLN GLN LEU LEU GLU HIS PHE LEU ARG SEQRES 2 A 101 GLN LEU GLN ARG LYS ASP PRO HIS GLY PHE PHE ALA PHE SEQRES 3 A 101 PRO VAL THR ASP ALA ILE ALA PRO GLY TYR SER MET ILE SEQRES 4 A 101 ILE LYS HIS PRO MET ASP PHE GLY THR MET LYS ASP LYS SEQRES 5 A 101 ILE VAL ALA ASN GLU TYR LYS SER VAL THR GLU PHE LYS SEQRES 6 A 101 ALA ASP PHE LYS LEU MET CYS ASP ASN ALA MET THR TYR SEQRES 7 A 101 ASN ARG PRO ASP THR VAL TYR TYR LYS LEU ALA LYS LYS SEQRES 8 A 101 ILE LEU HIS ALA GLY PHE LYS MET MET SER HET 67B A 201 23 HETNAM 67B N,N-DIMETHYL-3-(6-METHYL-7-OXO-6,7-DIHYDRO-1H- HETNAM 2 67B PYRROLO[2,3-C]PYRIDIN-4-YL)BENZAMIDE FORMUL 2 67B C17 H17 N3 O2 FORMUL 3 HOH *181(H2 O) HELIX 1 AA1 THR A 23 ARG A 38 1 16 HELIX 2 AA2 GLY A 56 ILE A 61 1 6 HELIX 3 AA3 ASP A 66 ALA A 76 1 11 HELIX 4 AA4 SER A 81 ASN A 100 1 20 HELIX 5 AA5 THR A 104 MET A 121 1 18 SITE 1 AC1 7 PHE A 44 PHE A 45 ILE A 53 ASN A 100 SITE 2 AC1 7 TYR A 106 LYS A 111 HOH A 305 CRYST1 24.640 34.000 39.490 68.56 74.31 72.95 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 0.040584 -0.012447 -0.007922 0.00000 SCALE2 0.000000 0.030764 -0.010066 0.00000 SCALE3 0.000000 0.000000 0.027675 0.00000