HEADER SIGNALING PROTEIN/INHIBITOR 20-FEB-17 5UVX
TITLE BRD4 BROMODOMAIN 2 WITH A-1359643
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: RESIDUES 352-457;
COMPND 5 SYNONYM: PROTEIN HUNK1;
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: BRD4, HUNK1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HELIX BUNDLE, SIGNALING PROTEIN-INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR C.H.PARK
REVDAT 2 06-MAR-24 5UVX 1 REMARK
REVDAT 1 21-JUN-17 5UVX 0
JRNL AUTH C.H.PARK
JRNL TITL BRD4 BROMODOMAIN 2 WITH A-1359643
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.53 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) : 1.53
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 40887
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) : 0.182
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.197
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950
REMARK 3 FREE R VALUE TEST SET COUNT : 2025
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.020
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) : 1.53
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.57
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2968
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2300
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2840
REMARK 3 BIN R VALUE (WORKING SET) : 0.2300
REMARK 3 BIN FREE R VALUE : 0.2430
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.31
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128
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 : 1745
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 58
REMARK 3 SOLVENT ATOMS : 283
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 25.04
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.61
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -7.22210
REMARK 3 B22 (A**2) : 1.99390
REMARK 3 B33 (A**2) : 5.22820
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
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) : 0.076
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.072
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.070
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.068
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 : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1893 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 2572 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 652 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 41 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 296 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1893 ; 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 : 217 ; 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 : 2444 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 0.92
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.77
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.17
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5UVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-17.
REMARK 100 THE DEPOSITION ID IS D_1000225714.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-MAR-16
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 : 17-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 : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 2.11.7
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41039
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530
REMARK 200 RESOLUTION RANGE LOW (A) : 48.500
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 6.400
REMARK 200 R MERGE (I) : 0.04600
REMARK 200 R SYM (I) : 0.04600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.67
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFER : 10 MM HEPES PH 7.5
REMARK 280 100 MM NACL 5 MM DTT CRYSTALLIZATION : 15 % (V/V) ETHANOL TRIS
REMARK 280 PH 7.0, VAPOR DIFFUSION, TEMPERATURE 277K
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 28.06750
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.40400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.52900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.40400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.06750
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.52900
REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 SER A 349
REMARK 465 SER B 349
REMARK 465 HIS B 350
REMARK 465 MET B 351
REMARK 465 GLU B 352
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8NM A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8NM B 501
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5UVS RELATED DB: PDB
REMARK 900 RELATED ID: 5UVU RELATED DB: PDB
REMARK 900 RELATED ID: 5UVT RELATED DB: PDB
REMARK 900 RELATED ID: 5UVV RELATED DB: PDB
REMARK 900 RELATED ID: 5UVZ RELATED DB: PDB
REMARK 900 RELATED ID: 5UVY RELATED DB: PDB
REMARK 900 RELATED ID: 5UVW RELATED DB: PDB
DBREF 5UVX A 352 457 UNP O60885 BRD4_HUMAN 352 457
DBREF 5UVX B 352 457 UNP O60885 BRD4_HUMAN 352 457
SEQADV 5UVX SER A 349 UNP O60885 EXPRESSION TAG
SEQADV 5UVX HIS A 350 UNP O60885 EXPRESSION TAG
SEQADV 5UVX MET A 351 UNP O60885 EXPRESSION TAG
SEQADV 5UVX SER B 349 UNP O60885 EXPRESSION TAG
SEQADV 5UVX HIS B 350 UNP O60885 EXPRESSION TAG
SEQADV 5UVX MET B 351 UNP O60885 EXPRESSION TAG
SEQRES 1 A 109 SER HIS MET GLU GLN LEU LYS CYS CYS SER GLY ILE LEU
SEQRES 2 A 109 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP
SEQRES 3 A 109 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU
SEQRES 4 A 109 HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO MET ASP MET
SEQRES 5 A 109 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG
SEQRES 6 A 109 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE
SEQRES 7 A 109 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL
SEQRES 8 A 109 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET
SEQRES 9 A 109 ARG PHE ALA LYS MET
SEQRES 1 B 109 SER HIS MET GLU GLN LEU LYS CYS CYS SER GLY ILE LEU
SEQRES 2 B 109 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP
SEQRES 3 B 109 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU
SEQRES 4 B 109 HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO MET ASP MET
SEQRES 5 B 109 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG
SEQRES 6 B 109 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE
SEQRES 7 B 109 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL
SEQRES 8 B 109 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET
SEQRES 9 B 109 ARG PHE ALA LYS MET
HET 8NM A 501 48
HET 8NM B 501 48
HETNAM 8NM N-[3-(6-METHYL-7-OXO-6,7-DIHYDRO-1H-PYRROLO[2,3-
HETNAM 2 8NM C]PYRIDIN-4-YL)-4-PHENOXYPHENYL]METHANESULFONAMIDE
FORMUL 3 8NM 2(C21 H19 N3 O4 S)
FORMUL 5 HOH *283(H2 O)
HELIX 1 AA1 HIS A 350 PHE A 365 1 16
HELIX 2 AA2 ALA A 366 LYS A 368 5 3
HELIX 3 AA3 HIS A 369 TRP A 374 1 6
HELIX 4 AA4 PRO A 375 TYR A 377 5 3
HELIX 5 AA5 ASP A 381 GLY A 386 1 6
HELIX 6 AA6 ASP A 389 ILE A 394 1 6
HELIX 7 AA7 ASP A 399 ALA A 409 1 11
HELIX 8 AA8 ASP A 414 ASN A 433 1 20
HELIX 9 AA9 HIS A 437 ALA A 455 1 19
HELIX 10 AB1 LEU B 354 PHE B 365 1 12
HELIX 11 AB2 ALA B 366 LYS B 368 5 3
HELIX 12 AB3 HIS B 369 TRP B 374 1 6
HELIX 13 AB4 PRO B 375 TYR B 377 5 3
HELIX 14 AB5 ASP B 381 GLY B 386 1 6
HELIX 15 AB6 ASP B 389 ILE B 394 1 6
HELIX 16 AB7 ASP B 399 ALA B 409 1 11
HELIX 17 AB8 ASP B 414 ASN B 433 1 20
HELIX 18 AB9 HIS B 437 LYS B 456 1 20
SITE 1 AC1 15 TRP A 374 PRO A 375 PHE A 376 LYS A 378
SITE 2 AC1 15 PRO A 379 VAL A 380 ASP A 381 LEU A 385
SITE 3 AC1 15 LEU A 387 ASN A 433 HIS A 437 MET A 442
SITE 4 AC1 15 HOH A 604 ASP B 436 HOH B 601
SITE 1 AC2 12 TRP A 374 TRP B 374 PRO B 375 PHE B 376
SITE 2 AC2 12 LYS B 378 PRO B 379 VAL B 380 ASP B 381
SITE 3 AC2 12 LEU B 385 ASN B 433 MET B 442 HOH B 606
CRYST1 56.135 65.058 72.808 90.00 90.00 90.00 P 21 21 21 8
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 0.017814 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015371 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013735 0.00000
(ATOM LINES ARE NOT SHOWN.)
END