HEADER GENE REGULATION 19-NOV-19 6V0X TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN BRD9 BOUND TO SUNITINIB 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; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS SUNITINIB, BRD9, MSWI/SNF, BAF, NON-BET, BRD, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,A.CHAN,J.Y.ZHU,E.SCHONBRUNN REVDAT 3 11-OCT-23 6V0X 1 COMPND REMARK HETNAM REVDAT 2 08-APR-20 6V0X 1 JRNL REVDAT 1 11-MAR-20 6V0X 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 18305 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 932 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 31.2410 - 2.8688 0.98 2673 146 0.1896 0.2175 REMARK 3 2 2.8688 - 2.2773 0.96 2478 134 0.2142 0.2356 REMARK 3 3 2.2773 - 1.9895 0.98 2501 136 0.1850 0.2144 REMARK 3 4 1.9895 - 1.8076 0.98 2453 132 0.1989 0.2155 REMARK 3 5 1.8076 - 1.6781 0.97 2458 133 0.2103 0.2294 REMARK 3 6 1.6781 - 1.5791 0.97 2432 126 0.2119 0.2425 REMARK 3 7 1.5791 - 1.5000 0.96 2378 125 0.2239 0.2573 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.16 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 54 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5491 13.8763 -2.9087 REMARK 3 T TENSOR REMARK 3 T11: 0.2379 T22: 0.2145 REMARK 3 T33: 0.2899 T12: -0.0289 REMARK 3 T13: -0.0167 T23: 0.0661 REMARK 3 L TENSOR REMARK 3 L11: 2.1663 L22: 5.3266 REMARK 3 L33: 2.6822 L12: 0.0368 REMARK 3 L13: 0.3605 L23: 1.4701 REMARK 3 S TENSOR REMARK 3 S11: -0.0324 S12: -0.1210 S13: -0.1935 REMARK 3 S21: 0.2241 S22: 0.1134 S23: 0.8125 REMARK 3 S31: 0.4930 S32: -0.2011 S33: 0.0202 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 55 THROUGH 60 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3893 29.8138 -4.8920 REMARK 3 T TENSOR REMARK 3 T11: 0.2725 T22: 0.3252 REMARK 3 T33: 0.2956 T12: -0.0621 REMARK 3 T13: 0.0476 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 6.1671 L22: 5.2460 REMARK 3 L33: 4.0571 L12: -4.0034 REMARK 3 L13: 0.5394 L23: 2.8773 REMARK 3 S TENSOR REMARK 3 S11: -0.1682 S12: 0.3565 S13: 0.2752 REMARK 3 S21: -0.5896 S22: -0.1350 S23: -0.3205 REMARK 3 S31: -0.0906 S32: 0.3359 S33: 0.1680 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 61 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7408 15.8780 -7.0191 REMARK 3 T TENSOR REMARK 3 T11: 0.2382 T22: 0.1627 REMARK 3 T33: 0.1829 T12: -0.0275 REMARK 3 T13: 0.0441 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 4.4665 L22: 4.2665 REMARK 3 L33: 2.2339 L12: 1.0877 REMARK 3 L13: 0.1284 L23: -0.5865 REMARK 3 S TENSOR REMARK 3 S11: -0.2645 S12: 0.4459 S13: -0.3706 REMARK 3 S21: -0.7231 S22: 0.2828 S23: 0.0322 REMARK 3 S31: 0.2277 S32: -0.0470 S33: -0.0607 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.1007 11.1986 3.9121 REMARK 3 T TENSOR REMARK 3 T11: 0.4473 T22: 0.3275 REMARK 3 T33: 0.5029 T12: 0.0248 REMARK 3 T13: 0.0600 T23: 0.1067 REMARK 3 L TENSOR REMARK 3 L11: 3.2976 L22: 3.8622 REMARK 3 L33: 6.7304 L12: 3.1318 REMARK 3 L13: 2.9741 L23: 4.2607 REMARK 3 S TENSOR REMARK 3 S11: 0.1698 S12: -0.1764 S13: -0.6667 REMARK 3 S21: 0.8231 S22: -0.0126 S23: 0.0878 REMARK 3 S31: 1.1049 S32: -0.0616 S33: -0.1662 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 6V0X 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_1000243946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-18 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) : 1.0 REMARK 200 MONOCHROMATOR : SI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 3.23700 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: 6UZF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 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 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 16.26500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.03100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.26500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.03100 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: 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: 6190 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 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 MET A 237 REMARK 465 SER A 238 REMARK 465 LYS A 239 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 146 CD REMARK 480 ARG A 154 CZ REMARK 480 LYS A 187 CE REMARK 480 GLU A 194 CD REMARK 480 LYS A 224 NZ REMARK 480 LYS A 228 CE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B49 A 301 DBREF 6V0X A 130 250 UNP Q9H8M2 BRD9_HUMAN 14 134 SEQADV 6V0X SER A 128 UNP Q9H8M2 EXPRESSION TAG SEQADV 6V0X 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 B49 A 301 29 HETNAM B49 N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2- HETNAM 2 B49 DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H- HETNAM 3 B49 PYRROLE-3-CARBO XAMIDE HETSYN B49 SUNITINIB FORMUL 2 B49 C22 H27 F N4 O2 FORMUL 3 HOH *91(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 236 1 17 SITE 1 AC1 12 PHE A 160 VAL A 165 ILE A 169 TYR A 173 SITE 2 AC1 12 ILE A 176 ASP A 188 ALA A 212 TYR A 215 SITE 3 AC1 12 ASN A 216 ARG A 217 TYR A 222 HOH A 406 CRYST1 32.530 112.062 30.823 90.00 90.00 90.00 P 21 21 2 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 0.030740 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032443 0.00000