HEADER TRANSCRIPTION/INHIBITOR 03-MAY-18 6DBC TITLE SECOND BROMODOMAIN OF HUMAN BRD2 WITH A TETRAHYDROQUINOLINE ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS BET, BRD2, BROMODOMAIN, INHIBITOR, COMPLEX, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.W.WHITE,M.YUN REVDAT 2 04-OCT-23 6DBC 1 REMARK REVDAT 1 13-NOV-19 6DBC 0 JRNL AUTH S.W.WHITE,M.YUN JRNL TITL SECOND BROMODOMAIN OF HUMAN BRD2 WITH A TETRAHYDROQUINOLINE JRNL TITL 2 ANALOGUE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.05 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 57429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620 REMARK 3 FREE R VALUE TEST SET COUNT : 2651 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 29.7350 - 2.7988 0.99 3097 150 0.1500 0.1372 REMARK 3 2 2.7988 - 2.2217 1.00 2977 144 0.1447 0.1506 REMARK 3 3 2.2217 - 1.9410 1.00 2933 142 0.1265 0.1297 REMARK 3 4 1.9410 - 1.7635 1.00 2906 139 0.1296 0.1333 REMARK 3 5 1.7635 - 1.6371 1.00 2901 141 0.1160 0.1144 REMARK 3 6 1.6371 - 1.5406 1.00 2898 140 0.1052 0.1174 REMARK 3 7 1.5406 - 1.4635 1.00 2858 140 0.1032 0.1177 REMARK 3 8 1.4635 - 1.3998 1.00 2905 140 0.1077 0.1310 REMARK 3 9 1.3998 - 1.3459 1.00 2880 139 0.1038 0.1196 REMARK 3 10 1.3459 - 1.2994 1.00 2865 139 0.1044 0.1211 REMARK 3 11 1.2994 - 1.2588 1.00 2861 138 0.1030 0.1217 REMARK 3 12 1.2588 - 1.2228 1.00 2859 139 0.1030 0.1094 REMARK 3 13 1.2228 - 1.1906 1.00 2836 138 0.1005 0.1039 REMARK 3 14 1.1906 - 1.1616 1.00 2869 140 0.1018 0.1253 REMARK 3 15 1.1616 - 1.1352 1.00 2881 138 0.1105 0.1204 REMARK 3 16 1.1352 - 1.1110 1.00 2828 137 0.1196 0.1403 REMARK 3 17 1.1110 - 1.0888 1.00 2854 137 0.1286 0.1548 REMARK 3 18 1.0888 - 1.0682 1.00 2845 138 0.1446 0.1463 REMARK 3 19 1.0682 - 1.0492 0.95 2725 132 0.1991 0.2195 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.42 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 : 0.005 1067 REMARK 3 ANGLE : 0.895 1435 REMARK 3 CHIRALITY : 0.077 139 REMARK 3 PLANARITY : 0.006 188 REMARK 3 DIHEDRAL : 3.851 866 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 6DBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57487 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 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: 5IG6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, POTASSIUM THICYANATE, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 26.19700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.09300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.19700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.09300 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: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 17.0 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 MET A 344 CG SD CE 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 LEU A 383 70.59 -100.01 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 780 DISTANCE = 6.16 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G3J A 508 DBREF 6DBC A 348 455 UNP P25440 BRD2_HUMAN 348 455 SEQADV 6DBC GLY A 341 UNP P25440 EXPRESSION TAG SEQADV 6DBC SER A 342 UNP P25440 EXPRESSION TAG SEQADV 6DBC HIS A 343 UNP P25440 EXPRESSION TAG SEQADV 6DBC MET A 344 UNP P25440 EXPRESSION TAG SEQADV 6DBC GLN A 345 UNP P25440 EXPRESSION TAG SEQADV 6DBC ASP A 346 UNP P25440 EXPRESSION TAG SEQADV 6DBC PRO A 347 UNP P25440 EXPRESSION TAG SEQRES 1 A 115 GLY SER HIS MET GLN ASP PRO GLU GLN LEU LYS HIS CYS SEQRES 2 A 115 ASN GLY ILE LEU LYS GLU LEU LEU SER LYS LYS HIS ALA SEQRES 3 A 115 ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA SER SEQRES 4 A 115 ALA LEU GLY LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS SEQRES 5 A 115 PRO MET ASP LEU SER THR VAL LYS ARG LYS MET GLU ASN SEQRES 6 A 115 ARG ASP TYR ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL SEQRES 7 A 115 ARG LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO SEQRES 8 A 115 ASP HIS ASP VAL VAL ALA MET ALA ARG LYS LEU GLN ASP SEQRES 9 A 115 VAL PHE GLU PHE ARG TYR ALA LYS MET PRO ASP HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET G3J A 508 27 HETNAM EDO 1,2-ETHANEDIOL HETNAM G3J 1-[(2S,4R)-4-[(2-CHLOROPHENYL)AMINO]-2-METHYL-6-(1H- HETNAM 2 G3J PYRAZOL-3-YL)-3,4-DIHYDROQUINOLIN-1(2H)-YL]ETHAN-1-ONE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 7(C2 H6 O2) FORMUL 9 G3J C21 H21 CL N4 O FORMUL 10 HOH *180(H2 O) HELIX 1 AA1 GLN A 345 LEU A 361 1 17 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 377 GLY A 382 1 6 HELIX 6 AA6 ASP A 385 ILE A 390 1 6 HELIX 7 AA7 ASP A 395 ASN A 405 1 11 HELIX 8 AA8 ASP A 410 ASN A 429 1 20 HELIX 9 AA9 HIS A 433 ALA A 451 1 19 SITE 1 AC1 4 LEU A 350 HOH A 604 HOH A 611 HOH A 687 SITE 1 AC2 7 ILE A 389 ILE A 390 LYS A 391 HIS A 392 SITE 2 AC2 7 ASN A 424 LYS A 427 ASP A 455 SITE 1 AC3 7 TYR A 368 LYS A 402 ASP A 407 GLU A 413 SITE 2 AC3 7 MET A 438 LYS A 441 HOH A 672 SITE 1 AC4 6 TYR A 426 ARG A 440 GLN A 443 ASP A 444 SITE 2 AC4 6 PHE A 448 HOH A 629 SITE 1 AC5 3 HIS A 433 ASP A 434 G3J A 508 SITE 1 AC6 6 LEU A 361 TYR A 373 HOH A 650 HOH A 653 SITE 2 AC6 6 HOH A 668 HOH A 689 SITE 1 AC7 3 LEU A 381 G3J A 508 HOH A 655 SITE 1 AC8 10 TRP A 370 PRO A 371 LEU A 383 ASN A 429 SITE 2 AC8 10 HIS A 433 VAL A 435 EDO A 505 EDO A 507 SITE 3 AC8 10 HOH A 609 HOH A 655 CRYST1 52.394 72.186 31.975 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 0.019086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031274 0.00000