HEADER GENE REGULATION 07-MAY-21 7MRH TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN (BD1) OF HUMAN BRDT BOUND TITLE 2 TO NC-II-259 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN TESTIS-SPECIFIC PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CANCER/TESTIS ANTIGEN 9,CT9,RING3-LIKE PROTEIN; 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: BRDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLIC-HIS KEYWDS BRDT, BRD, BET, GENE REGULATION, CONTRACEPTIVE, CANCER EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAN,E.SCHONBRUNN REVDAT 3 18-OCT-23 7MRH 1 REMARK REVDAT 2 24-AUG-22 7MRH 1 JRNL REVDAT 1 03-AUG-22 7MRH 0 JRNL AUTH X.GUAN,N.CHERYALA,R.M.KARIM,A.CHAN,N.BERNDT,J.QI,G.I.GEORG, JRNL AUTH 2 E.SCHONBRUNN JRNL TITL BIVALENT BET BROMODOMAIN INHIBITORS CONFER INCREASED POTENCY JRNL TITL 2 AND SELECTIVITY FOR BRDT VIA PROTEIN CONFORMATIONAL JRNL TITL 3 PLASTICITY. JRNL REF J.MED.CHEM. V. 65 10441 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35867655 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00453 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 19601 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.610 REMARK 3 FREE R VALUE TEST SET COUNT : 1099 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 33.9300 - 3.9600 0.95 2401 142 0.1426 0.1668 REMARK 3 2 3.9600 - 3.1400 0.96 2326 139 0.1548 0.2037 REMARK 3 3 3.1400 - 2.7500 0.97 2314 137 0.1955 0.2467 REMARK 3 4 2.7500 - 2.4900 0.98 2345 139 0.1934 0.2705 REMARK 3 5 2.4900 - 2.3200 0.98 2333 139 0.1891 0.2865 REMARK 3 6 2.3200 - 2.1800 0.94 2227 132 0.1847 0.2214 REMARK 3 7 2.1800 - 2.0700 0.96 2283 136 0.2048 0.2473 REMARK 3 8 2.0700 - 1.9800 0.98 2273 135 0.2388 0.2955 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.70 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -11.2117 2.0769 -21.6515 REMARK 3 T TENSOR REMARK 3 T11: 0.2409 T22: 0.2148 REMARK 3 T33: 0.2322 T12: -0.0025 REMARK 3 T13: -0.0045 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.0288 L22: 0.6832 REMARK 3 L33: 0.2651 L12: 0.2107 REMARK 3 L13: 0.0581 L23: 0.0572 REMARK 3 S TENSOR REMARK 3 S11: 0.0306 S12: -0.1174 S13: -0.0021 REMARK 3 S21: 0.2134 S22: -0.0308 S23: 0.0123 REMARK 3 S31: 0.0187 S32: 0.0002 S33: 0.0106 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 7MRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-19 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19605 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 33.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.292 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.32 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.050 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: 4KCX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE TRIBASIC PH REMARK 280 7.0, 20% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 14.91000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 GLY A 25 REMARK 465 ALA A 26 REMARK 465 ALA A 27 REMARK 465 GLU A 137 REMARK 465 GLY B 25 REMARK 465 ALA B 26 REMARK 465 ALA B 27 REMARK 465 GLU B 137 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 LYS A 90 CG CD CE NZ REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 GLN A 135 CG CD OE1 NE2 REMARK 470 GLN B 135 CG CD OE1 NE2 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 349 O HOH A 362 2.14 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 GLN B 135 98.01 -60.12 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 B 384 DISTANCE = 7.63 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZMJ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZMJ B 201 DBREF 7MRH A 29 137 UNP Q58F21 BRDT_HUMAN 29 137 DBREF 7MRH B 29 137 UNP Q58F21 BRDT_HUMAN 29 137 SEQADV 7MRH GLY A 25 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH ALA A 26 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH ALA A 27 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH SER A 28 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH GLY B 25 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH ALA B 26 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH ALA B 27 UNP Q58F21 EXPRESSION TAG SEQADV 7MRH SER B 28 UNP Q58F21 EXPRESSION TAG SEQRES 1 A 113 GLY ALA ALA SER THR ASN GLN LEU GLN TYR LEU GLN LYS SEQRES 2 A 113 VAL VAL LEU LYS ASP LEU TRP LYS HIS SER PHE SER TRP SEQRES 3 A 113 PRO PHE GLN ARG PRO VAL ASP ALA VAL LYS LEU GLN LEU SEQRES 4 A 113 PRO ASP TYR TYR THR ILE ILE LYS ASN PRO MET ASP LEU SEQRES 5 A 113 ASN THR ILE LYS LYS ARG LEU GLU ASN LYS TYR TYR ALA SEQRES 6 A 113 LYS ALA SER GLU CYS ILE GLU ASP PHE ASN THR MET PHE SEQRES 7 A 113 SER ASN CYS TYR LEU TYR ASN LYS PRO GLY ASP ASP ILE SEQRES 8 A 113 VAL LEU MET ALA GLN ALA LEU GLU LYS LEU PHE MET GLN SEQRES 9 A 113 LYS LEU SER GLN MET PRO GLN GLU GLU SEQRES 1 B 113 GLY ALA ALA SER THR ASN GLN LEU GLN TYR LEU GLN LYS SEQRES 2 B 113 VAL VAL LEU LYS ASP LEU TRP LYS HIS SER PHE SER TRP SEQRES 3 B 113 PRO PHE GLN ARG PRO VAL ASP ALA VAL LYS LEU GLN LEU SEQRES 4 B 113 PRO ASP TYR TYR THR ILE ILE LYS ASN PRO MET ASP LEU SEQRES 5 B 113 ASN THR ILE LYS LYS ARG LEU GLU ASN LYS TYR TYR ALA SEQRES 6 B 113 LYS ALA SER GLU CYS ILE GLU ASP PHE ASN THR MET PHE SEQRES 7 B 113 SER ASN CYS TYR LEU TYR ASN LYS PRO GLY ASP ASP ILE SEQRES 8 B 113 VAL LEU MET ALA GLN ALA LEU GLU LYS LEU PHE MET GLN SEQRES 9 B 113 LYS LEU SER GLN MET PRO GLN GLU GLU HET ZMJ A 201 24 HET ZMJ B 201 24 HETNAM ZMJ N-[3-(2-METHYL-1-OXO-1,2-DIHYDROISOQUINOLIN-4-YL) HETNAM 2 ZMJ PHENYL]ETHANESULFONAMIDE FORMUL 3 ZMJ 2(C18 H18 N2 O3 S) FORMUL 5 HOH *168(H2 O) HELIX 1 AA1 SER A 28 VAL A 38 1 11 HELIX 2 AA2 VAL A 38 HIS A 46 1 9 HELIX 3 AA3 SER A 49 GLN A 53 5 5 HELIX 4 AA4 ASP A 65 ILE A 70 1 6 HELIX 5 AA5 ASP A 75 ASN A 85 1 11 HELIX 6 AA6 LYS A 90 ASN A 109 1 20 HELIX 7 AA7 ASP A 113 GLN A 132 1 20 HELIX 8 AA8 THR B 29 VAL B 38 1 10 HELIX 9 AA9 VAL B 38 HIS B 46 1 9 HELIX 10 AB1 SER B 49 GLN B 53 5 5 HELIX 11 AB2 ASP B 65 ILE B 70 1 6 HELIX 12 AB3 ASP B 75 ASN B 85 1 11 HELIX 13 AB4 LYS B 90 ASN B 109 1 20 HELIX 14 AB5 ASP B 113 GLN B 132 1 20 SITE 1 AC1 11 TRP A 50 PRO A 51 PHE A 52 ARG A 54 SITE 2 AC1 11 PRO A 55 VAL A 56 ASP A 57 LYS A 60 SITE 3 AC1 11 LEU A 61 ASN A 109 HOH A 313 SITE 1 AC2 12 TRP B 50 PRO B 51 PHE B 52 ARG B 54 SITE 2 AC2 12 PRO B 55 VAL B 56 ASP B 57 LYS B 60 SITE 3 AC2 12 LEU B 61 ASN B 109 HOH B 315 HOH B 320 CRYST1 66.640 29.820 73.220 90.00 98.56 90.00 P 1 21 1 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 0.015006 0.000000 0.002260 0.00000 SCALE2 0.000000 0.033535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013811 0.00000