PDB Short entry for 4QYL HEADER PROTEIN BINDING 24-JUL-14 4QYL TITLE CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH A TITLE 2 HISTONE H2AK5AC PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEREGRIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: BROMODOMAIN (UNP RESIDUES 629-742); COMPND 5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1, PROTEIN COMPND 6 BR140; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H2A TYPE 1; COMPND 10 CHAIN: E, F, G, H; COMPND 11 FRAGMENT: HISTONE H2AK5AC PEPTIDE (UNP RESIDUES 2-13); COMPND 12 SYNONYM: H2A.1, HISTONE H2A/P; COMPND 13 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: BR140, BRPF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2DE3PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST15; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS BROMODOMAIN-PHD FINGER PROTEIN 1 (BRPF1), HISTONE ACETYLTRANSFERASE KEYWDS 2 (HAT), MONOCYTIC LEUKEMIA ZINC-FINGER (MOZ), EPIGENETICS, CHROMATIN KEYWDS 3 READER, BROMODOMAIN, HISTONE POST-TRANSCRIPTIONAL MODIFICATION (PTM) KEYWDS 4 READER DOMAIN, ACETYLLYSINE, NUCLEUS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.Y.LUBULA,K.C.GLASS REVDAT 5 06-DEC-23 4QYL 1 REMARK REVDAT 4 20-SEP-23 4QYL 1 REMARK SEQADV LINK REVDAT 3 17-DEC-14 4QYL 1 JRNL REVDAT 2 22-OCT-14 4QYL 1 JRNL REVDAT 1 24-SEP-14 4QYL 0 JRNL AUTH M.Y.LUBULA,B.E.ECKENROTH,S.CARLSON,A.POPLAWSKI,M.CHRUSZCZ, JRNL AUTH 2 K.C.GLASS JRNL TITL STRUCTURAL INSIGHTS INTO RECOGNITION OF ACETYLATED HISTONE JRNL TITL 2 LIGANDS BY THE BRPF1 BROMODOMAIN. JRNL REF FEBS LETT. V. 588 3844 2014 JRNL REFN ISSN 0014-5793 JRNL PMID 25281266 JRNL DOI 10.1016/J.FEBSLET.2014.09.028 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48421 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2587 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3536 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 197 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4087 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 722 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.66000 REMARK 3 B33 (A**2) : -1.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.095 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4354 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4147 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5881 ; 1.775 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9554 ; 1.351 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 539 ; 5.890 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;33.971 ;24.764 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 778 ;12.263 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ; 8.287 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 617 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5060 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1033 ; 0.007 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 117 B 1 117 7510 0.07 0.05 REMARK 3 2 A 1 117 C 1 117 7370 0.08 0.05 REMARK 3 3 A 1 117 D 1 117 7384 0.07 0.05 REMARK 3 4 B 1 117 C 1 117 7214 0.07 0.05 REMARK 3 5 B 1 117 D 1 117 7228 0.07 0.05 REMARK 3 6 C 1 117 D 1 117 7159 0.09 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4QYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48421 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.38600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3RCW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4SO4, 0.1 M MES MONOHYDRATE, REMARK 280 PH 6.5, 30% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEG) 5000, REMARK 280 1% PROPYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.79050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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: 3 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: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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: 4 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: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H 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 ARG E 11 REMARK 465 ALA E 12 REMARK 465 ARG F 11 REMARK 465 ALA F 12 REMARK 465 ARG G 11 REMARK 465 ALA G 12 REMARK 465 ARG H 11 REMARK 465 ALA H 12 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 LYS A 45 CG CD CE NZ REMARK 470 LYS C 45 CG CD CE NZ REMARK 470 ARG C 105 NE CZ NH1 NH2 REMARK 470 ILE C 116 CB CG1 CG2 CD1 REMARK 470 LYS D 45 CG CD CE NZ REMARK 470 LYS D 85 CG CD CE NZ REMARK 470 ILE D 116 CG1 CG2 CD1 REMARK 470 ARG E 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG F 3 CG CD NE CZ NH1 NH2 REMARK 470 ARG G 3 CG CD NE CZ NH1 NH2 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 OE1 GLN C 99 O HOH C 501 2.05 REMARK 500 OE1 GLN D 99 O HOH D 398 2.11 REMARK 500 O HOH C 379 O HOH C 409 2.12 REMARK 500 OD1 ASN B 26 O HOH B 436 2.14 REMARK 500 O HOH B 441 O HOH B 488 2.17 REMARK 500 NE2 GLN D 99 O HOH D 424 2.19 REMARK 500 O HOH B 486 O HOH C 415 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 401 O HOH C 444 2748 2.08 REMARK 500 OE1 GLN D 99 O HOH A 420 1565 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ASP B 66 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP C 117 CB - CG - OD2 ANGL. DEV. = -6.2 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 ILE C 116 65.60 67.43 REMARK 500 ILE D 116 50.27 -141.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE C 116 ASP C 117 42.53 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QYD RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH THE HISTONE H4K12AC PEPTIDE DBREF 4QYL A 4 117 UNP P55201 BRPF1_HUMAN 629 742 DBREF 4QYL B 4 117 UNP P55201 BRPF1_HUMAN 629 742 DBREF 4QYL C 4 117 UNP P55201 BRPF1_HUMAN 629 742 DBREF 4QYL D 4 117 UNP P55201 BRPF1_HUMAN 629 742 DBREF 4QYL E 1 12 UNP P0C0S8 H2A1_HUMAN 2 13 DBREF 4QYL F 1 12 UNP P0C0S8 H2A1_HUMAN 2 13 DBREF 4QYL G 1 12 UNP P0C0S8 H2A1_HUMAN 2 13 DBREF 4QYL H 1 12 UNP P0C0S8 H2A1_HUMAN 2 13 SEQADV 4QYL GLY A 1 UNP P55201 EXPRESSION TAG SEQADV 4QYL PRO A 2 UNP P55201 EXPRESSION TAG SEQADV 4QYL LEU A 3 UNP P55201 EXPRESSION TAG SEQADV 4QYL GLY B 1 UNP P55201 EXPRESSION TAG SEQADV 4QYL PRO B 2 UNP P55201 EXPRESSION TAG SEQADV 4QYL LEU B 3 UNP P55201 EXPRESSION TAG SEQADV 4QYL GLY C 1 UNP P55201 EXPRESSION TAG SEQADV 4QYL PRO C 2 UNP P55201 EXPRESSION TAG SEQADV 4QYL LEU C 3 UNP P55201 EXPRESSION TAG SEQADV 4QYL GLY D 1 UNP P55201 EXPRESSION TAG SEQADV 4QYL PRO D 2 UNP P55201 EXPRESSION TAG SEQADV 4QYL LEU D 3 UNP P55201 EXPRESSION TAG SEQRES 1 A 117 GLY PRO LEU GLN LEU THR PRO PHE LEU ILE LEU LEU ARG SEQRES 2 A 117 LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY ASN SEQRES 3 A 117 ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO ASP SEQRES 4 A 117 TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE THR SEQRES 5 A 117 MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN PHE SEQRES 6 A 117 ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER ASN SEQRES 7 A 117 CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR ARG SEQRES 8 A 117 ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL LEU SEQRES 9 A 117 ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY ILE ASP SEQRES 1 B 117 GLY PRO LEU GLN LEU THR PRO PHE LEU ILE LEU LEU ARG SEQRES 2 B 117 LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY ASN SEQRES 3 B 117 ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO ASP SEQRES 4 B 117 TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE THR SEQRES 5 B 117 MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN PHE SEQRES 6 B 117 ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER ASN SEQRES 7 B 117 CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR ARG SEQRES 8 B 117 ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL LEU SEQRES 9 B 117 ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY ILE ASP SEQRES 1 C 117 GLY PRO LEU GLN LEU THR PRO PHE LEU ILE LEU LEU ARG SEQRES 2 C 117 LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY ASN SEQRES 3 C 117 ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO ASP SEQRES 4 C 117 TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE THR SEQRES 5 C 117 MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN PHE SEQRES 6 C 117 ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER ASN SEQRES 7 C 117 CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR ARG SEQRES 8 C 117 ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL LEU SEQRES 9 C 117 ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY ILE ASP SEQRES 1 D 117 GLY PRO LEU GLN LEU THR PRO PHE LEU ILE LEU LEU ARG SEQRES 2 D 117 LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY ASN SEQRES 3 D 117 ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO ASP SEQRES 4 D 117 TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE THR SEQRES 5 D 117 MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN PHE SEQRES 6 D 117 ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER ASN SEQRES 7 D 117 CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR ARG SEQRES 8 D 117 ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL LEU SEQRES 9 D 117 ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY ILE ASP SEQRES 1 E 12 SER GLY ARG GLY ALY GLN GLY GLY LYS ALA ARG ALA SEQRES 1 F 12 SER GLY ARG GLY ALY GLN GLY GLY LYS ALA ARG ALA SEQRES 1 G 12 SER GLY ARG GLY ALY GLN GLY GLY LYS ALA ARG ALA SEQRES 1 H 12 SER GLY ARG GLY ALY GLN GLY GLY LYS ALA ARG ALA MODRES 4QYL ALY E 5 LYS N(6)-ACETYLLYSINE MODRES 4QYL ALY F 5 LYS N(6)-ACETYLLYSINE MODRES 4QYL ALY G 5 LYS N(6)-ACETYLLYSINE MODRES 4QYL ALY H 5 LYS N(6)-ACETYLLYSINE HET ALY E 5 12 HET ALY F 5 12 HET ALY G 5 12 HET ALY H 5 12 HET SO4 A 201 5 HET SO4 B 201 5 HET SO4 C 201 5 HET SO4 D 201 5 HETNAM ALY N(6)-ACETYLLYSINE HETNAM SO4 SULFATE ION FORMUL 5 ALY 4(C8 H16 N2 O3) FORMUL 9 SO4 4(O4 S 2-) FORMUL 13 HOH *722(H2 O) HELIX 1 1 THR A 6 ASP A 23 1 18 HELIX 2 2 ASP A 39 ILE A 44 1 6 HELIX 3 3 ASP A 49 ALA A 59 1 11 HELIX 4 4 ASN A 64 ASN A 83 1 20 HELIX 5 5 THR A 87 MET A 114 1 28 HELIX 6 6 THR B 6 ASP B 23 1 18 HELIX 7 7 ASP B 39 ILE B 44 1 6 HELIX 8 8 ASP B 49 ALA B 59 1 11 HELIX 9 9 ASN B 64 ASN B 83 1 20 HELIX 10 10 THR B 87 MET B 114 1 28 HELIX 11 11 THR C 6 ASP C 23 1 18 HELIX 12 12 ASP C 39 ILE C 44 1 6 HELIX 13 13 ASP C 49 ALA C 59 1 11 HELIX 14 14 ASN C 64 ASN C 83 1 20 HELIX 15 15 THR C 87 MET C 114 1 28 HELIX 16 16 THR D 6 LYS D 22 1 17 HELIX 17 17 ASP D 39 ILE D 44 1 6 HELIX 18 18 ASP D 49 ALA D 59 1 11 HELIX 19 19 ASN D 64 ASN D 83 1 20 HELIX 20 20 THR D 87 MET D 114 1 28 LINK C GLY E 4 N ALY E 5 1555 1555 1.33 LINK C ALY E 5 N GLN E 6 1555 1555 1.33 LINK C GLY F 4 N ALY F 5 1555 1555 1.32 LINK C ALY F 5 N GLN F 6 1555 1555 1.30 LINK C GLY G 4 N ALY G 5 1555 1555 1.33 LINK C ALY G 5 N AGLN G 6 1555 1555 1.31 LINK C ALY G 5 N BGLN G 6 1555 1555 1.34 LINK C GLY H 4 N ALY H 5 1555 1555 1.33 LINK C ALY H 5 N GLN H 6 1555 1555 1.31 SITE 1 AC1 7 ARG A 91 ARG A 95 HOH A 314 HOH A 316 SITE 2 AC1 7 ARG D 109 GLN D 110 LYS D 113 SITE 1 AC2 9 ARG B 91 ARG B 95 HOH B 339 HOH B 427 SITE 2 AC2 9 HOH B 484 ARG C 109 GLN C 110 LYS C 113 SITE 3 AC2 9 HOH C 321 SITE 1 AC3 8 ARG B 109 GLN B 110 LYS B 113 HOH B 304 SITE 2 AC3 8 ARG C 91 ARG C 95 HOH C 334 HOH C 463 SITE 1 AC4 8 ARG A 109 GLN A 110 LYS A 113 HOH A 309 SITE 2 AC4 8 ARG D 91 ARG D 95 HOH D 360 HOH D 422 CRYST1 60.908 55.581 82.135 90.00 93.58 90.00 P 1 21 1 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 0.016418 0.000000 0.001027 0.00000 SCALE2 0.000000 0.017992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012199 0.00000