HEADER TRANSCRIPTION/PROTEIN BINDING 30-NOV-11 3UVX TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX TITLE 2 WITH A DIACETYLATED HISTONE 4 PEPTIDE (H4K12ACK16AC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 44-168; COMPND 5 SYNONYM: PROTEIN HUNK1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DIACETYLATED HISTONE 4 PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: PEPTIDE (H4K12ACK16AC); COMPND 11 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: HUMAN HISTONE 4 PEPTIDE (UNIPROT: P62805) RESIDUES SOURCE 16 11-21 ACETYLATED ON K12 AND K16 KEYWDS BROMODOMAIN, BROMODOMAIN CONTAINING PROTEIN 4, CAP, HUNK1, MCAP, KEYWDS 2 MITOTIC CHROMOSOME ASSOCIATED PROTEIN, PEPTIDE COMPLEX, STRUCTURAL KEYWDS 3 GENOMICS CONSORTIUM, SGC, TRANSCRIPTION-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.FILIPPAKOPOULOS,S.PICAUD,T.KEATES,E.UGOCHUKWU,F.VON DELFT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,J.WEIGELT,C.BOUNTRA,S.KNAPP,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 7 09-OCT-24 3UVX 1 REMARK REVDAT 6 06-DEC-23 3UVX 1 REMARK REVDAT 5 13-SEP-23 3UVX 1 REMARK SEQADV LINK REVDAT 4 31-JAN-18 3UVX 1 SOURCE AUTHOR REVDAT 3 29-AUG-12 3UVX 1 COMPND REVDAT 2 11-APR-12 3UVX 1 JRNL REVDAT 1 25-JAN-12 3UVX 0 JRNL AUTH P.FILIPPAKOPOULOS,S.PICAUD,M.MANGOS,T.KEATES,J.P.LAMBERT, JRNL AUTH 2 D.BARSYTE-LOVEJOY,I.FELLETAR,R.VOLKMER,S.MULLER,T.PAWSON, JRNL AUTH 3 A.C.GINGRAS,C.H.ARROWSMITH,S.KNAPP JRNL TITL HISTONE RECOGNITION AND LARGE-SCALE STRUCTURAL ANALYSIS OF JRNL TITL 2 THE HUMAN BROMODOMAIN FAMILY. JRNL REF CELL(CAMBRIDGE,MASS.) V. 149 214 2012 JRNL REFN ISSN 0092-8674 JRNL PMID 22464331 JRNL DOI 10.1016/J.CELL.2012.02.013 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 10766 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 517 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 656 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : 1.06000 REMARK 3 B33 (A**2) : -0.24000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1165 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 817 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1562 ; 1.471 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2006 ; 0.951 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 132 ; 5.959 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;38.096 ;25.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 202 ;14.969 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;18.329 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 168 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1238 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 216 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 42 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): 37.9590 32.5757 10.6343 REMARK 3 T TENSOR REMARK 3 T11: 0.0701 T22: 0.0247 REMARK 3 T33: 0.0602 T12: -0.0077 REMARK 3 T13: 0.0190 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 1.1386 L22: 0.3315 REMARK 3 L33: 0.8215 L12: -0.3307 REMARK 3 L13: -0.4115 L23: 0.1216 REMARK 3 S TENSOR REMARK 3 S11: -0.1162 S12: -0.0146 S13: -0.2236 REMARK 3 S21: 0.0592 S22: 0.0216 S23: 0.0597 REMARK 3 S31: 0.0987 S32: -0.0043 S33: 0.0946 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 91 A 168 REMARK 3 ORIGIN FOR THE GROUP (A): 38.4847 39.7834 13.6362 REMARK 3 T TENSOR REMARK 3 T11: 0.0767 T22: 0.0548 REMARK 3 T33: 0.0482 T12: -0.0083 REMARK 3 T13: 0.0057 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.5216 L22: 0.3236 REMARK 3 L33: 0.8671 L12: -0.0637 REMARK 3 L13: -0.2201 L23: 0.4833 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.0677 S13: -0.0260 REMARK 3 S21: 0.0599 S22: -0.0266 S23: 0.0272 REMARK 3 S31: 0.0737 S32: 0.0461 S33: 0.0250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 3UVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.52 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 24.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : 0.11200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.61700 REMARK 200 R SYM FOR SHELL (I) : 0.61700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: ENSEMBLE OF 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.35M NAFORTMATE 20% PEG 3350 10% REMARK 280 ETGLY, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K 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 21.97000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.97000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.19000 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 300 REMARK: MONOMER 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 HIS B 18 REMARK 465 ARG B 19 REMARK 465 LYS B 20 REMARK 465 VAL B 21 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 SER A 42 OG REMARK 470 LYS A 72 CE NZ REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 ARG B 17 CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY B 11 CA - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 GLY B 11 O - C - N ANGL. DEV. = -18.1 DEGREES REMARK 500 ALY B 12 C - N - CA ANGL. DEV. = 21.3 DEGREES REMARK 500 ALY B 12 O - C - N ANGL. DEV. = -22.9 DEGREES REMARK 500 ALA B 15 O - C - N ANGL. DEV. = -12.2 DEGREES REMARK 500 ALY B 16 O - C - N ANGL. DEV. = -21.9 DEGREES 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 LEU A 94 71.42 -114.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY B 11 12.06 REMARK 500 ALY B 12 31.52 REMARK 500 ALY B 16 27.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 30 O REMARK 620 2 ASN A 61 OD1 84.6 REMARK 620 3 GLN A 64 OE1 102.2 93.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 2 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 49 OE1 REMARK 620 2 HOH A 202 O 103.9 REMARK 620 3 HOH A 203 O 101.2 107.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 3 DBREF 3UVX A 44 168 UNP O60885 BRD4_HUMAN 44 168 DBREF 3UVX B 11 21 PDB 3UVX 3UVX 11 21 SEQADV 3UVX SER A 42 UNP O60885 EXPRESSION TAG SEQADV 3UVX 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 SEQRES 1 B 11 GLY ALY GLY GLY ALA ALY ARG HIS ARG LYS VAL MODRES 3UVX ALY B 12 LYS N(6)-ACETYLLYSINE MODRES 3UVX ALY B 16 LYS N(6)-ACETYLLYSINE HET ALY B 12 12 HET ALY B 16 12 HET NA A 1 1 HET NA A 2 1 HET EDO A 169 4 HET FMT A 170 3 HET FMT A 171 3 HET FMT A 3 3 HETNAM ALY N(6)-ACETYLLYSINE HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ALY 2(C8 H16 N2 O3) FORMUL 3 NA 2(NA 1+) FORMUL 5 EDO C2 H6 O2 FORMUL 6 FMT 3(C H2 O2) FORMUL 9 HOH *99(H2 O) HELIX 1 1 THR A 60 VAL A 69 1 10 HELIX 2 2 VAL A 69 LYS A 76 1 8 HELIX 3 3 ALA A 80 GLN A 84 5 5 HELIX 4 4 ASP A 96 ILE A 101 1 6 HELIX 5 5 ASP A 106 ASN A 116 1 11 HELIX 6 6 ASN A 121 ASN A 140 1 20 HELIX 7 7 ASP A 144 ASN A 162 1 19 LINK C GLY B 11 N ALY B 12 1555 1555 1.34 LINK C ALY B 12 N GLY B 13 1555 1555 1.36 LINK C ALA B 15 N ALY B 16 1555 1555 1.34 LINK C ALY B 16 N ARG B 17 1555 1555 1.38 LINK NA NA A 1 O HOH A 30 1555 1555 2.36 LINK NA NA A 1 OD1 ASN A 61 1555 1555 2.23 LINK NA NA A 1 OE1 GLN A 64 1555 1555 2.26 LINK NA NA A 2 OE1 GLU A 49 1555 1555 2.94 LINK NA NA A 2 O HOH A 202 1555 1555 2.47 LINK NA NA A 2 O HOH A 203 1555 1555 2.61 SITE 1 AC1 5 HOH A 30 ASN A 61 GLN A 64 TYR A 137 SITE 2 AC1 5 ASN A 140 SITE 1 AC2 4 GLU A 49 HOH A 202 HOH A 203 HOH A 231 SITE 1 AC3 6 ILE A 100 ILE A 101 LYS A 102 THR A 103 SITE 2 AC3 6 ASN A 135 HOH A 226 SITE 1 AC4 5 THR A 60 GLN A 62 ASN A 121 ALA A 122 SITE 2 AC4 5 HOH A 231 SITE 1 AC5 6 HOH A 8 SER A 51 ASN A 52 LYS A 57 SITE 2 AC5 6 ASN A 116 TYR A 118 SITE 1 AC6 2 ARG A 113 ASP A 128 CRYST1 43.940 52.380 57.620 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 0.022758 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017355 0.00000