HEADER GENE REGULATION 19-NOV-19 6V14 TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN BRD9 BOUND TO TP472 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIPL KEYWDS BRD9, MSWI/SNF, BAF, NON-BET, BRD, TP472, TP-472, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,A.CHAN,E.SCHONBRUNN REVDAT 4 11-OCT-23 6V14 1 REMARK REVDAT 3 01-JUL-20 6V14 1 REMARK REVDAT 2 08-APR-20 6V14 1 JRNL REVDAT 1 11-MAR-20 6V14 0 JRNL AUTH R.M.KARIM,A.CHAN,J.Y.ZHU,E.SCHONBRUNN JRNL TITL STRUCTURAL BASIS OF INHIBITOR SELECTIVITY IN THE BRD7/9 JRNL TITL 2 SUBFAMILY OF BROMODOMAINS. JRNL REF J.MED.CHEM. V. 63 3227 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32091206 JRNL DOI 10.1021/ACS.JMEDCHEM.9B01980 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260_3260 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 11091 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 555 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 34.9040 - 2.6981 0.99 2656 140 0.1365 0.1284 REMARK 3 2 2.6981 - 2.1417 1.00 2664 140 0.1495 0.2106 REMARK 3 3 2.1417 - 1.8710 1.00 2672 141 0.1493 0.1913 REMARK 3 4 1.8710 - 1.7000 0.95 2544 134 0.1590 0.2308 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.50 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 22 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2492 -6.7726 7.5935 REMARK 3 T TENSOR REMARK 3 T11: 0.1819 T22: 0.1410 REMARK 3 T33: 0.0826 T12: -0.0063 REMARK 3 T13: -0.0059 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.3765 L22: 3.9404 REMARK 3 L33: 1.9596 L12: -1.1011 REMARK 3 L13: 0.4267 L23: -1.6137 REMARK 3 S TENSOR REMARK 3 S11: -0.0246 S12: -0.3194 S13: -0.1098 REMARK 3 S21: 0.4617 S22: 0.1635 S23: 0.1652 REMARK 3 S31: 0.0573 S32: -0.0973 S33: -0.1225 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8549 3.6560 -4.7403 REMARK 3 T TENSOR REMARK 3 T11: 0.0926 T22: 0.0803 REMARK 3 T33: 0.1210 T12: -0.0129 REMARK 3 T13: 0.0111 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.0628 L22: 1.5852 REMARK 3 L33: 0.1514 L12: 0.3472 REMARK 3 L13: 0.1298 L23: 0.0678 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: 0.0964 S13: 0.0827 REMARK 3 S21: -0.0302 S22: 0.0745 S23: 0.0176 REMARK 3 S31: -0.1085 S32: -0.0994 S33: -0.0521 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3013 -4.5819 -8.7226 REMARK 3 T TENSOR REMARK 3 T11: 0.0947 T22: 0.0932 REMARK 3 T33: 0.0867 T12: -0.0048 REMARK 3 T13: -0.0002 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 1.2926 L22: 0.8231 REMARK 3 L33: 0.9305 L12: -0.2442 REMARK 3 L13: -0.0071 L23: -0.0894 REMARK 3 S TENSOR REMARK 3 S11: 0.0615 S12: 0.1309 S13: -0.0840 REMARK 3 S21: -0.0833 S22: -0.0028 S23: -0.0121 REMARK 3 S31: 0.0160 S32: 0.0275 S33: -0.0555 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.0005 3.7509 -2.5628 REMARK 3 T TENSOR REMARK 3 T11: 0.1166 T22: 0.1639 REMARK 3 T33: 0.1395 T12: -0.0279 REMARK 3 T13: -0.0068 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.7260 L22: 2.8767 REMARK 3 L33: 2.8507 L12: -0.6564 REMARK 3 L13: 0.8533 L23: -0.6154 REMARK 3 S TENSOR REMARK 3 S11: 0.1667 S12: -0.3691 S13: -0.0979 REMARK 3 S21: 0.3178 S22: 0.0581 S23: -0.1200 REMARK 3 S31: -0.0751 S32: 0.1552 S33: -0.1642 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 6V14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000243952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 34.904 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.597 REMARK 200 R MERGE (I) : 0.02100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.64 REMARK 200 R MERGE FOR SHELL (I) : 0.07200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.120 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: PDBID 3HME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M BIS-TRIS (PH 5.5), REMARK 280 AND 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 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 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 SER A 128 REMARK 465 MET A 129 REMARK 465 LEU A 130 REMARK 465 LYS A 131 REMARK 465 LEU A 132 REMARK 465 SER A 133 REMARK 465 ALA A 134 REMARK 465 GLU A 135 REMARK 465 ASN A 136 REMARK 465 GLU A 137 REMARK 465 GLU A 240 REMARK 465 ARG A 241 REMARK 465 LEU A 242 REMARK 465 LEU A 243 REMARK 465 ALA A 244 REMARK 465 LEU A 245 REMARK 465 LYS A 246 REMARK 465 ARG A 247 REMARK 465 SER A 248 REMARK 465 MET A 249 REMARK 465 SER A 250 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 466 O HOH A 493 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 QMG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 DBREF 6V14 A 130 250 UNP Q9H8M2 BRD9_HUMAN 14 134 SEQADV 6V14 SER A 128 UNP Q9H8M2 EXPRESSION TAG SEQADV 6V14 MET A 129 UNP Q9H8M2 EXPRESSION TAG SEQRES 1 A 123 SER MET LEU LYS LEU SER ALA GLU ASN GLU SER THR PRO SEQRES 2 A 123 ILE GLN GLN LEU LEU GLU HIS PHE LEU ARG GLN LEU GLN SEQRES 3 A 123 ARG LYS ASP PRO HIS GLY PHE PHE ALA PHE PRO VAL THR SEQRES 4 A 123 ASP ALA ILE ALA PRO GLY TYR SER MET ILE ILE LYS HIS SEQRES 5 A 123 PRO MET ASP PHE GLY THR MET LYS ASP LYS ILE VAL ALA SEQRES 6 A 123 ASN GLU TYR LYS SER VAL THR GLU PHE LYS ALA ASP PHE SEQRES 7 A 123 LYS LEU MET CYS ASP ASN ALA MET THR TYR ASN ARG PRO SEQRES 8 A 123 ASP THR VAL TYR TYR LYS LEU ALA LYS LYS ILE LEU HIS SEQRES 9 A 123 ALA GLY PHE LYS MET MET SER LYS GLU ARG LEU LEU ALA SEQRES 10 A 123 LEU LYS ARG SER MET SER HET QMG A 301 25 HET EDO A 302 4 HETNAM QMG 3-(6-ACETYLPYRROLO[1,2-A]PYRIMIDIN-8-YL)-N-CYCLOPROPYL- HETNAM 2 QMG 4-METHYLBENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 QMG C20 H19 N3 O2 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *119(H2 O) HELIX 1 AA1 THR A 139 LYS A 155 1 17 HELIX 2 AA2 GLY A 172 ILE A 177 1 6 HELIX 3 AA3 ASP A 182 ALA A 192 1 11 HELIX 4 AA4 SER A 197 ASN A 216 1 20 HELIX 5 AA5 THR A 220 MET A 237 1 18 SITE 1 AC1 9 PHE A 160 VAL A 165 ILE A 169 ASN A 216 SITE 2 AC1 9 TYR A 222 LYS A 227 HOH A 416 HOH A 471 SITE 3 AC1 9 HOH A 480 SITE 1 AC2 7 ARG A 150 MET A 213 THR A 214 ASN A 216 SITE 2 AC2 7 ARG A 217 PRO A 218 HOH A 452 CRYST1 23.270 33.860 37.680 104.10 102.10 105.91 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 0.042974 0.012247 0.013860 0.00000 SCALE2 0.000000 0.030709 0.010378 0.00000 SCALE3 0.000000 0.000000 0.028650 0.00000