HEADER PROTEIN BINDING 22-APR-16 5JI8 TITLE CRYSTAL STRUCTURE OF THE BRD9 BROMODOMAIN AND HIT 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 137-239; COMPND 5 SYNONYM: RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8; COMPND 6 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-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS BRD9, BROMODOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.WANG,F.LI,H.BAO,J.LI,J.WU,K.RUAN REVDAT 3 08-NOV-23 5JI8 1 REMARK REVDAT 2 17-AUG-16 5JI8 1 JRNL REVDAT 1 22-JUN-16 5JI8 0 JRNL AUTH N.WANG,F.LI,H.BAO,J.LI,J.WU,K.RUAN JRNL TITL NMR FRAGMENT SCREENING HIT INDUCES PLASTICITY OF BRD7/9 JRNL TITL 2 BROMODOMAINS JRNL REF CHEMBIOCHEM V. 17 1456 2016 JRNL REFN ESSN 1439-7633 JRNL PMID 27194508 JRNL DOI 10.1002/CBIC.201600184 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 3 NUMBER OF REFLECTIONS : 18442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 918 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 28.1125 - 2.7166 0.97 2775 177 0.1481 0.1623 REMARK 3 2 2.7166 - 2.1565 0.97 2841 138 0.1503 0.1804 REMARK 3 3 2.1565 - 1.8840 0.95 2746 128 0.1434 0.1674 REMARK 3 4 1.8840 - 1.7117 0.95 2774 157 0.1500 0.1665 REMARK 3 5 1.7117 - 1.5891 0.91 2647 151 0.1486 0.1829 REMARK 3 6 1.5891 - 1.4954 0.74 2151 97 0.1586 0.1899 REMARK 3 7 1.4954 - 1.4205 0.55 1590 70 0.1870 0.2166 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.08 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 : 0.009 851 REMARK 3 ANGLE : 0.907 1149 REMARK 3 CHIRALITY : 0.066 121 REMARK 3 PLANARITY : 0.007 144 REMARK 3 DIHEDRAL : 18.624 318 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 0.8912 0.7266 1.3584 REMARK 3 T TENSOR REMARK 3 T11: 0.0752 T22: 0.0872 REMARK 3 T33: 0.0686 T12: 0.0092 REMARK 3 T13: -0.0054 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 4.0718 L22: 2.8556 REMARK 3 L33: 2.2993 L12: 0.2847 REMARK 3 L13: -0.5373 L23: 0.3490 REMARK 3 S TENSOR REMARK 3 S11: -0.0688 S12: -0.1772 S13: 0.0807 REMARK 3 S21: 0.0031 S22: 0.0438 S23: 0.0326 REMARK 3 S31: 0.0778 S32: 0.0149 S33: 0.0232 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 5JI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20295 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.20200 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: 3HME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH6.4, 27% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 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 GLU A 137 REMARK 465 SER A 138 REMARK 465 LYS A 239 REMARK 465 LEU A 240 REMARK 465 GLU A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 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 ARG A 154 CZ NH1 NH2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 ARG A 217 CD NE CZ NH1 NH2 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 471 O HOH A 487 2.12 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 554 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 555 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 556 DISTANCE = 6.96 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6KT A 301 DBREF 5JI8 A 137 239 UNP Q9H8M2 BRD9_HUMAN 137 239 SEQADV 5JI8 LEU A 240 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 GLU A 241 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 HIS A 242 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 HIS A 243 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 HIS A 244 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 HIS A 245 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 HIS A 246 UNP Q9H8M2 EXPRESSION TAG SEQADV 5JI8 HIS A 247 UNP Q9H8M2 EXPRESSION TAG SEQRES 1 A 111 GLU SER THR PRO ILE GLN GLN LEU LEU GLU HIS PHE LEU SEQRES 2 A 111 ARG GLN LEU GLN ARG LYS ASP PRO HIS GLY PHE PHE ALA SEQRES 3 A 111 PHE PRO VAL THR ASP ALA ILE ALA PRO GLY TYR SER MET SEQRES 4 A 111 ILE ILE LYS HIS PRO MET ASP PHE GLY THR MET LYS ASP SEQRES 5 A 111 LYS ILE VAL ALA ASN GLU TYR LYS SER VAL THR GLU PHE SEQRES 6 A 111 LYS ALA ASP PHE LYS LEU MET CYS ASP ASN ALA MET THR SEQRES 7 A 111 TYR ASN ARG PRO ASP THR VAL TYR TYR LYS LEU ALA LYS SEQRES 8 A 111 LYS ILE LEU HIS ALA GLY PHE LYS MET MET SER LYS LEU SEQRES 9 A 111 GLU HIS HIS HIS HIS HIS HIS HET 6KT A 301 20 HETNAM 6KT 2-AMINO-1,3-BENZOTHIAZOLE-6-CARBOXAMIDE FORMUL 2 6KT C8 H7 N3 O S FORMUL 3 HOH *156(H2 O) HELIX 1 AA1 THR A 139 ARG A 154 1 16 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 SER A 238 1 19 SITE 1 AC1 7 PHE A 160 PHE A 161 VAL A 165 ILE A 169 SITE 2 AC1 7 ASN A 216 TYR A 222 HOH A 401 CRYST1 24.498 34.090 39.519 70.09 75.28 73.24 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 0.040820 -0.012291 -0.007500 0.00000 SCALE2 0.000000 0.030635 -0.009234 0.00000 SCALE3 0.000000 0.000000 0.027326 0.00000