HEADER TRANSCRIPTION 14-OCT-16 5M39 TITLE CRYSTAL STRUCTURE OF BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A, B; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, BRD4 BD1, EPIGENETIC, HISTONE READER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR D.KESSLER,M.MAYER,H.ENGELHARDT,B.WOLKERSTORFER,L.GEIST REVDAT 3 17-JAN-24 5M39 1 REMARK REVDAT 2 22-NOV-17 5M39 1 JRNL REVDAT 1 27-SEP-17 5M39 0 JRNL AUTH L.GEIST,M.MAYER,X.L.COCKCROFT,B.WOLKERSTORFER,D.KESSLER, JRNL AUTH 2 H.ENGELHARDT,D.B.MCCONNELL,R.KONRAT JRNL TITL DIRECT NMR PROBING OF HYDRATION SHELLS OF PROTEIN LIGAND JRNL TITL 2 INTERFACES AND ITS APPLICATION TO DRUG DESIGN. JRNL REF J. MED. CHEM. V. 60 8708 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28910100 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00845 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 46692 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 2318 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.31 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3541 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2360 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3372 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.77 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 169 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2088 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.94010 REMARK 3 B22 (A**2) : -2.56620 REMARK 3 B33 (A**2) : 0.62610 REMARK 3 B12 (A**2) : 0.52550 REMARK 3 B13 (A**2) : -1.16550 REMARK 3 B23 (A**2) : -0.66320 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.200 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.083 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.080 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.081 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.079 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2192 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2984 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 752 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 67 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 296 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2192 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 275 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2768 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.98 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.78 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -3.1962 1.6967 -14.9204 REMARK 3 T TENSOR REMARK 3 T11: -0.0391 T22: -0.0564 REMARK 3 T33: -0.0142 T12: 0.0133 REMARK 3 T13: -0.0117 T23: -0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.7386 L22: 0.5838 REMARK 3 L33: 1.4543 L12: 0.0239 REMARK 3 L13: -1.0592 L23: 0.0558 REMARK 3 S TENSOR REMARK 3 S11: 0.0848 S12: 0.1049 S13: 0.0570 REMARK 3 S21: -0.0083 S22: -0.0807 S23: -0.0364 REMARK 3 S31: -0.0696 S32: -0.0696 S33: -0.0041 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 0.9357 21.7064 -39.8445 REMARK 3 T TENSOR REMARK 3 T11: -0.0373 T22: -0.0556 REMARK 3 T33: -0.0163 T12: -0.0032 REMARK 3 T13: -0.0110 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 1.8403 L22: 0.9034 REMARK 3 L33: 1.0728 L12: -0.3175 REMARK 3 L13: -0.7822 L23: 0.4832 REMARK 3 S TENSOR REMARK 3 S11: 0.0788 S12: -0.0771 S13: 0.0661 REMARK 3 S21: -0.0293 S22: -0.0825 S23: 0.0322 REMARK 3 S31: -0.0519 S32: 0.0071 S33: 0.0038 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5M39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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) : 0.90002 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 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47067 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.377 REMARK 200 RESOLUTION RANGE LOW (A) : 38.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31800 REMARK 200 R SYM FOR SHELL (I) : 0.31800 REMARK 200 FOR SHELL : 2.100 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: 2OSS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG3350 0.2M DISODIUM MALONATE REMARK 280 0.01 M HEPES, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K 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, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 THR A 166 REMARK 465 GLU A 167 REMARK 465 GLU A 168 REMARK 465 GLU B 168 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7EA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7EA B 201 DBREF 5M39 A 42 168 UNP O60885 BRD4_HUMAN 42 168 DBREF 5M39 B 42 168 UNP O60885 BRD4_HUMAN 42 168 SEQADV 5M39 MET A 43 UNP O60885 THR 43 CONFLICT SEQADV 5M39 MET B 43 UNP O60885 THR 43 CONFLICT 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 SEQRES 1 B 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 B 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 B 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 B 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 B 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 B 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 B 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 B 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 B 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 B 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET 7EA A 201 20 HET 7EA B 201 20 HETNAM 7EA 6-(3,4-DIMETHOXYPHENYL)-3-METHYL-[1,2,4]TRIAZOLO[4,3- HETNAM 2 7EA B]PYRIDAZINE FORMUL 3 7EA 2(C14 H14 N4 O2) FORMUL 5 HOH *266(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 LYS A 76 1 8 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 96 ILE A 101 1 6 HELIX 5 AA5 ASP A 106 ASN A 116 1 11 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 ASN A 162 1 19 HELIX 8 AA8 THR B 60 VAL B 69 1 10 HELIX 9 AA9 VAL B 69 LYS B 76 1 8 HELIX 10 AB1 ALA B 80 GLN B 84 5 5 HELIX 11 AB2 ASP B 96 ILE B 101 1 6 HELIX 12 AB3 ASP B 106 ASN B 116 1 11 HELIX 13 AB4 ASN B 121 ASN B 140 1 20 HELIX 14 AB5 ASP B 144 ASN B 162 1 19 SITE 1 AC1 6 TRP A 81 PHE A 83 VAL A 87 LEU A 92 SITE 2 AC1 6 ASN A 140 HOH A 302 SITE 1 AC2 6 PHE A 79 TRP B 81 PHE B 83 LEU B 92 SITE 2 AC2 6 ASN B 140 HOH B 301 CRYST1 30.379 39.506 57.972 99.71 105.05 89.90 P 1 2 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 0.032917 -0.000057 0.008978 0.00000 SCALE2 0.000000 0.025313 0.004477 0.00000 SCALE3 0.000000 0.000000 0.018140 0.00000