HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 29-SEP-15 5E0R TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF BRD4 IN COMPLEX WITH AYC COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; 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: BRD4, HUNK1; 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: PNIC28-BSA4 KEYWDS TRANSCRIPTION-TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DONG,A.CAFLISCH REVDAT 2 10-JAN-24 5E0R 1 REMARK REVDAT 1 12-OCT-16 5E0R 0 JRNL AUTH J.DONG,A.CAFLISH JRNL TITL CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF BRD4 IN JRNL TITL 2 COMPLEX WITH AYC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 27220 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1342 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 38.9982 - 2.9134 0.99 2880 144 0.1674 0.1929 REMARK 3 2 2.9134 - 2.3125 0.99 2727 143 0.1762 0.1945 REMARK 3 3 2.3125 - 2.0202 0.99 2723 140 0.1541 0.1910 REMARK 3 4 2.0202 - 1.8355 0.99 2693 145 0.1611 0.1826 REMARK 3 5 1.8355 - 1.7039 0.99 2672 166 0.1663 0.2213 REMARK 3 6 1.7039 - 1.6035 0.99 2648 149 0.1702 0.1947 REMARK 3 7 1.6035 - 1.5232 0.99 2687 137 0.1647 0.1773 REMARK 3 8 1.5232 - 1.4569 0.98 2652 135 0.1820 0.2187 REMARK 3 9 1.4569 - 1.4008 0.90 2429 105 0.2104 0.2427 REMARK 3 10 1.4008 - 1.3524 0.66 1767 78 0.2780 0.3025 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) : 19.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.07 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 1269 REMARK 3 ANGLE : 1.315 1745 REMARK 3 CHIRALITY : 0.051 173 REMARK 3 PLANARITY : 0.007 221 REMARK 3 DIHEDRAL : 17.317 475 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): 11.8169 -3.0253 -8.1222 REMARK 3 T TENSOR REMARK 3 T11: 0.0615 T22: 0.0776 REMARK 3 T33: 0.0806 T12: 0.0030 REMARK 3 T13: 0.0044 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.4506 L22: 0.6510 REMARK 3 L33: 0.8310 L12: 0.0073 REMARK 3 L13: -0.1387 L23: -0.0537 REMARK 3 S TENSOR REMARK 3 S11: -0.0168 S12: -0.0150 S13: -0.0108 REMARK 3 S21: 0.0184 S22: 0.0042 S23: 0.0150 REMARK 3 S31: 0.0589 S32: 0.0175 S33: -0.0007 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 5E0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214156. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-14 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 : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JUN 17, 2015 REMARK 200 BUILT=20150617 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.352 REMARK 200 RESOLUTION RANGE LOW (A) : 38.982 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.31100 REMARK 200 R SYM FOR SHELL (I) : 0.31100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: 4PCI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.20M SODIUM NITRATE, 20% PEG 3350, REMARK 280 10% ETHYLENE GLYCOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.38800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.98200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.26900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.98200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.38800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.26900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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 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 317 O HOH A 407 1.83 REMARK 500 O HOH A 337 O HOH A 420 1.99 REMARK 500 O HOH A 351 O HOH A 422 2.01 REMARK 500 O HOH A 392 O HOH A 419 2.07 REMARK 500 NZ LYS A 72 O HOH A 301 2.08 REMARK 500 NZ LYS A 76 O HOH A 302 2.17 REMARK 500 O HOH A 384 O HOH A 417 2.18 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 ASN A 52 100.61 -161.87 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 5J5 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5J5 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5J5 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5J5 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5J5 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 206 DBREF 5E0R A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 5E0R SER A 42 UNP O60885 EXPRESSION TAG SEQADV 5E0R MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET 5J5 A 201 27 HET 5J5 A 202 27 HET 5J5 A 203 27 HET 5J5 A 204 27 HET 5J5 A 205 27 HET DMS A 206 4 HETNAM 5J5 2-[(CHLOROACETYL)AMINO]-5-[(E)-(4-SULFOPHENYL) HETNAM 2 5J5 DIAZENYL]BENZENESULFONIC ACID HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 5J5 5(C14 H12 CL N3 O7 S2) FORMUL 7 DMS C2 H6 O S FORMUL 8 HOH *146(H2 O) HELIX 1 AA1 THR A 60 THR A 73 1 14 HELIX 2 AA2 HIS A 77 GLN A 84 5 8 HELIX 3 AA3 ASP A 96 ILE A 101 1 6 HELIX 4 AA4 ASP A 106 ASN A 116 1 11 HELIX 5 AA5 ASN A 121 ASN A 140 1 20 HELIX 6 AA6 ASP A 144 GLU A 163 1 20 SITE 1 AC1 18 MET A 43 ASN A 52 ASN A 54 GLN A 62 SITE 2 AC1 18 HIS A 77 GLN A 78 PHE A 79 ASN A 121 SITE 3 AC1 18 ALA A 122 GLN A 123 ILE A 126 ILE A 161 SITE 4 AC1 18 GLU A 167 5J5 A 204 HOH A 308 HOH A 323 SITE 5 AC1 18 HOH A 357 HOH A 376 SITE 1 AC2 17 LYS A 57 TRP A 81 PRO A 82 GLN A 85 SITE 2 AC2 17 PRO A 86 ASP A 88 LYS A 91 ASP A 96 SITE 3 AC2 17 LYS A 99 ILE A 100 ASP A 145 ILE A 146 SITE 4 AC2 17 HOH A 320 HOH A 331 HOH A 371 HOH A 425 SITE 5 AC2 17 HOH A 438 SITE 1 AC3 15 ASN A 61 GLN A 64 TYR A 65 ARG A 68 SITE 2 AC3 15 LYS A 72 THR A 73 PRO A 142 GLY A 143 SITE 3 AC3 15 VAL A 147 GLU A 151 LYS A 160 5J5 A 205 SITE 4 AC3 15 HOH A 303 HOH A 345 HOH A 358 SITE 1 AC4 10 PRO A 48 GLU A 49 ASN A 52 ARG A 58 SITE 2 AC4 10 PHE A 79 ASN A 121 GLN A 123 5J5 A 201 SITE 3 AC4 10 HOH A 306 HOH A 307 SITE 1 AC5 13 SER A 51 ARG A 68 ASN A 116 PRO A 142 SITE 2 AC5 13 GLY A 143 GLU A 163 PRO A 165 5J5 A 203 SITE 3 AC5 13 HOH A 304 HOH A 313 HOH A 332 HOH A 401 SITE 4 AC5 13 HOH A 422 SITE 1 AC6 2 ASN A 140 HOH A 318 CRYST1 36.776 44.538 77.964 90.00 90.00 90.00 P 21 21 21 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 0.027192 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012826 0.00000