HEADER PROTEIN BINDING 24-MAR-15 4YYK TITLE CRYSTAL STRUCTURE OF BRD9 BROMODOMAIN BOUND TO A CROTONYLLYSINE TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 9; COMPND 3 CHAIN: A, B, D, E; COMPND 4 FRAGMENT: BROMODOMAIN (UNP RESIDUES 17-123); COMPND 5 SYNONYM: RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8, BRD9; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H4; COMPND 9 CHAIN: C, F; COMPND 10 FRAGMENT: N-TERMINAL TAIL (UNP RESIDUES 2-12); COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: LYSINE RESIDUES CROTONYLATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BRD9, UNQ3040/PRO9856; 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: PRSF; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS BROMODOMAIN-CROTONYLLYSINE COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.TANG,S.BELLON,A.G.COCHRAN,F.POY REVDAT 5 15-NOV-23 4YYK 1 REMARK REVDAT 4 27-SEP-23 4YYK 1 JRNL REMARK REVDAT 3 14-OCT-15 4YYK 1 JRNL REVDAT 2 30-SEP-15 4YYK 1 JRNL REVDAT 1 16-SEP-15 4YYK 0 JRNL AUTH E.M.FLYNN,O.W.HUANG,F.POY,M.OPPIKOFER,S.F.BELLON,Y.TANG, JRNL AUTH 2 A.G.COCHRAN JRNL TITL A SUBSET OF HUMAN BROMODOMAINS RECOGNIZES BUTYRYLLYSINE AND JRNL TITL 2 CROTONYLLYSINE HISTONE PEPTIDE MODIFICATIONS. JRNL REF STRUCTURE V. 23 1801 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 26365797 JRNL DOI 10.1016/J.STR.2015.08.004 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 34482 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1851 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1928 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3372 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.52000 REMARK 3 B22 (A**2) : 8.16000 REMARK 3 B33 (A**2) : -6.64000 REMARK 3 B12 (A**2) : -0.84000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : -2.82000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.036 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.153 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3458 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4634 ; 2.846 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 410 ; 7.772 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;37.941 ;23.784 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 624 ;20.322 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;24.631 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 484 ; 0.210 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2584 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1658 ; 3.122 ; 2.457 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2062 ; 3.973 ; 3.667 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1800 ; 3.560 ; 2.601 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.879 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : H, H-K, -L REMARK 3 TWIN FRACTION : 0.121 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 22 A 122 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0322 -0.1050 -34.2189 REMARK 3 T TENSOR REMARK 3 T11: 0.0155 T22: 0.0100 REMARK 3 T33: 0.0285 T12: -0.0022 REMARK 3 T13: -0.0115 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.8113 L22: 0.6094 REMARK 3 L33: 0.8678 L12: 0.1610 REMARK 3 L13: 0.4153 L23: -0.2193 REMARK 3 S TENSOR REMARK 3 S11: 0.0193 S12: 0.0133 S13: 0.0077 REMARK 3 S21: 0.0309 S22: -0.0345 S23: -0.0152 REMARK 3 S31: 0.0442 S32: -0.0256 S33: 0.0152 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 : B 22 B 122 REMARK 3 ORIGIN FOR THE GROUP (A): -0.1549 23.3179 -66.4459 REMARK 3 T TENSOR REMARK 3 T11: 0.0421 T22: 0.0048 REMARK 3 T33: 0.0299 T12: 0.0101 REMARK 3 T13: 0.0061 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.0343 L22: 0.4710 REMARK 3 L33: 0.4690 L12: 0.0479 REMARK 3 L13: -0.4183 L23: -0.2807 REMARK 3 S TENSOR REMARK 3 S11: -0.0054 S12: -0.0026 S13: -0.0822 REMARK 3 S21: -0.0208 S22: -0.0081 S23: -0.0308 REMARK 3 S31: -0.0563 S32: -0.0020 S33: 0.0135 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 22 D 122 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3333 0.6140 -1.8211 REMARK 3 T TENSOR REMARK 3 T11: 0.0065 T22: 0.0076 REMARK 3 T33: 0.0252 T12: 0.0019 REMARK 3 T13: -0.0012 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.7747 L22: 0.7606 REMARK 3 L33: 0.7985 L12: 0.1325 REMARK 3 L13: 0.5267 L23: 0.2407 REMARK 3 S TENSOR REMARK 3 S11: -0.0056 S12: -0.0294 S13: 0.0278 REMARK 3 S21: -0.0388 S22: -0.0076 S23: -0.0031 REMARK 3 S31: 0.0278 S32: -0.0122 S33: 0.0131 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 22 E 122 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3435 22.9709 30.3937 REMARK 3 T TENSOR REMARK 3 T11: 0.0546 T22: 0.0044 REMARK 3 T33: 0.0383 T12: -0.0114 REMARK 3 T13: 0.0030 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 0.9763 L22: 0.2354 REMARK 3 L33: 0.7834 L12: -0.0246 REMARK 3 L13: -0.7408 L23: 0.2422 REMARK 3 S TENSOR REMARK 3 S11: -0.0243 S12: 0.0077 S13: -0.0275 REMARK 3 S21: -0.0179 S22: -0.0115 S23: 0.0295 REMARK 3 S31: -0.0196 S32: -0.0082 S33: 0.0357 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: NULL REMARK 4 REMARK 4 4YYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-12 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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.61700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: PDB ENTRY 3HME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.5, 15% W/V PEG550 MME, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 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 GLY A 16 REMARK 465 SER A 17 REMARK 465 ALA A 18 REMARK 465 GLU A 19 REMARK 465 ASN A 20 REMARK 465 GLU A 21 REMARK 465 LYS A 123 REMARK 465 GLY B 16 REMARK 465 SER B 17 REMARK 465 ALA B 18 REMARK 465 GLU B 19 REMARK 465 ASN B 20 REMARK 465 GLU B 21 REMARK 465 LYS B 123 REMARK 465 SER C 1 REMARK 465 GLY C 2 REMARK 465 ARG C 3 REMARK 465 LEU C 10 REMARK 465 GLY C 11 REMARK 465 GLY D 16 REMARK 465 SER D 17 REMARK 465 ALA D 18 REMARK 465 GLU D 19 REMARK 465 ASN D 20 REMARK 465 GLU D 21 REMARK 465 LYS D 123 REMARK 465 GLY E 16 REMARK 465 SER E 17 REMARK 465 ALA E 18 REMARK 465 GLU E 19 REMARK 465 ASN E 20 REMARK 465 GLU E 21 REMARK 465 LYS E 123 REMARK 465 SER F 1 REMARK 465 GLY F 2 REMARK 465 ARG F 3 REMARK 465 LEU F 10 REMARK 465 GLY F 11 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 57 CE1 TYR A 57 CZ 0.118 REMARK 500 ASP A 66 C ASP A 66 O 0.117 REMARK 500 PHE B 45 C PHE B 45 O 0.209 REMARK 500 GLY E 43 N GLY E 43 CA 0.105 REMARK 500 PHE E 89 CB PHE E 89 CG 0.105 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 LEU A 28 CB - CG - CD1 ANGL. DEV. = -11.6 DEGREES REMARK 500 MET A 70 CG - SD - CE ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP A 72 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 LEU A 91 CB - CG - CD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ASP B 51 CB - CG - OD2 ANGL. DEV. = 8.5 DEGREES REMARK 500 LEU B 91 CB - CG - CD1 ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP B 94 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 LEU D 33 CB - CG - CD1 ANGL. DEV. = -13.2 DEGREES REMARK 500 PRO D 48 C - N - CA ANGL. DEV. = -12.5 DEGREES REMARK 500 LEU D 91 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 MET D 97 CG - SD - CE ANGL. DEV. = 10.0 DEGREES REMARK 500 LEU E 36 CB - CG - CD2 ANGL. DEV. = 15.2 DEGREES REMARK 500 ASP E 66 CB - CG - OD2 ANGL. DEV. = -8.5 DEGREES REMARK 500 PHE E 67 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 PHE E 67 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP E 94 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP E 94 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ILE E 113 CG1 - CB - CG2 ANGL. DEV. = -15.4 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 LYS A 39 -2.56 -59.71 REMARK 500 ILE A 60 -47.42 -134.49 REMARK 500 ASP A 103 5.38 -63.16 REMARK 500 ASN B 77 59.23 35.85 REMARK 500 PRO B 102 -34.11 -39.91 REMARK 500 ILE D 74 -74.08 -64.33 REMARK 500 VAL D 75 -32.06 -35.29 REMARK 500 ASP E 40 61.46 -108.09 REMARK 500 PHE E 44 -36.40 -33.88 REMARK 500 PRO E 55 112.90 -34.39 REMARK 500 ALA E 76 33.47 -79.00 REMARK 500 ASN E 77 54.01 12.79 REMARK 500 ARG E 101 132.35 -38.64 REMARK 500 ASP E 103 8.35 -66.80 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 PHE D 32 -11.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YY4 RELATED DB: PDB REMARK 900 RELATED ID: 4YY6 RELATED DB: PDB REMARK 900 RELATED ID: 4YYD RELATED DB: PDB REMARK 900 RELATED ID: 4YYG RELATED DB: PDB REMARK 900 RELATED ID: 4YYH RELATED DB: PDB REMARK 900 RELATED ID: 4YYI RELATED DB: PDB REMARK 900 RELATED ID: 4YYJ RELATED DB: PDB REMARK 900 RELATED ID: 4YYM RELATED DB: PDB REMARK 900 RELATED ID: 4YYN RELATED DB: PDB DBREF 4YYK A 17 123 UNP Q9H8M2 BRD9_HUMAN 17 123 DBREF 4YYK B 17 123 UNP Q9H8M2 BRD9_HUMAN 17 123 DBREF 4YYK C 1 11 UNP P62805 H4_HUMAN 2 12 DBREF 4YYK D 17 123 UNP Q9H8M2 BRD9_HUMAN 17 123 DBREF 4YYK E 17 123 UNP Q9H8M2 BRD9_HUMAN 17 123 DBREF 4YYK F 1 11 UNP P62805 H4_HUMAN 2 12 SEQADV 4YYK GLY A 16 UNP Q9H8M2 EXPRESSION TAG SEQADV 4YYK GLY B 16 UNP Q9H8M2 EXPRESSION TAG SEQADV 4YYK GLY D 16 UNP Q9H8M2 EXPRESSION TAG SEQADV 4YYK GLY E 16 UNP Q9H8M2 EXPRESSION TAG SEQRES 1 A 108 GLY SER ALA GLU ASN GLU SER THR PRO ILE GLN GLN LEU SEQRES 2 A 108 LEU GLU HIS PHE LEU ARG GLN LEU GLN ARG LYS ASP PRO SEQRES 3 A 108 HIS GLY PHE PHE ALA PHE PRO VAL THR ASP ALA ILE ALA SEQRES 4 A 108 PRO GLY TYR SER MET ILE ILE LYS HIS PRO MET ASP PHE SEQRES 5 A 108 GLY THR MET LYS ASP LYS ILE VAL ALA ASN GLU TYR LYS SEQRES 6 A 108 SER VAL THR GLU PHE LYS ALA ASP PHE LYS LEU MET CYS SEQRES 7 A 108 ASP ASN ALA MET THR TYR ASN ARG PRO ASP THR VAL TYR SEQRES 8 A 108 TYR LYS LEU ALA LYS LYS ILE LEU HIS ALA GLY PHE LYS SEQRES 9 A 108 MET MET SER LYS SEQRES 1 B 108 GLY SER ALA GLU ASN GLU SER THR PRO ILE GLN GLN LEU SEQRES 2 B 108 LEU GLU HIS PHE LEU ARG GLN LEU GLN ARG LYS ASP PRO SEQRES 3 B 108 HIS GLY PHE PHE ALA PHE PRO VAL THR ASP ALA ILE ALA SEQRES 4 B 108 PRO GLY TYR SER MET ILE ILE LYS HIS PRO MET ASP PHE SEQRES 5 B 108 GLY THR MET LYS ASP LYS ILE VAL ALA ASN GLU TYR LYS SEQRES 6 B 108 SER VAL THR GLU PHE LYS ALA ASP PHE LYS LEU MET CYS SEQRES 7 B 108 ASP ASN ALA MET THR TYR ASN ARG PRO ASP THR VAL TYR SEQRES 8 B 108 TYR LYS LEU ALA LYS LYS ILE LEU HIS ALA GLY PHE LYS SEQRES 9 B 108 MET MET SER LYS SEQRES 1 C 11 SER GLY ARG GLY KCR GLY GLY KCR GLY LEU GLY SEQRES 1 D 108 GLY SER ALA GLU ASN GLU SER THR PRO ILE GLN GLN LEU SEQRES 2 D 108 LEU GLU HIS PHE LEU ARG GLN LEU GLN ARG LYS ASP PRO SEQRES 3 D 108 HIS GLY PHE PHE ALA PHE PRO VAL THR ASP ALA ILE ALA SEQRES 4 D 108 PRO GLY TYR SER MET ILE ILE LYS HIS PRO MET ASP PHE SEQRES 5 D 108 GLY THR MET LYS ASP LYS ILE VAL ALA ASN GLU TYR LYS SEQRES 6 D 108 SER VAL THR GLU PHE LYS ALA ASP PHE LYS LEU MET CYS SEQRES 7 D 108 ASP ASN ALA MET THR TYR ASN ARG PRO ASP THR VAL TYR SEQRES 8 D 108 TYR LYS LEU ALA LYS LYS ILE LEU HIS ALA GLY PHE LYS SEQRES 9 D 108 MET MET SER LYS SEQRES 1 E 108 GLY SER ALA GLU ASN GLU SER THR PRO ILE GLN GLN LEU SEQRES 2 E 108 LEU GLU HIS PHE LEU ARG GLN LEU GLN ARG LYS ASP PRO SEQRES 3 E 108 HIS GLY PHE PHE ALA PHE PRO VAL THR ASP ALA ILE ALA SEQRES 4 E 108 PRO GLY TYR SER MET ILE ILE LYS HIS PRO MET ASP PHE SEQRES 5 E 108 GLY THR MET LYS ASP LYS ILE VAL ALA ASN GLU TYR LYS SEQRES 6 E 108 SER VAL THR GLU PHE LYS ALA ASP PHE LYS LEU MET CYS SEQRES 7 E 108 ASP ASN ALA MET THR TYR ASN ARG PRO ASP THR VAL TYR SEQRES 8 E 108 TYR LYS LEU ALA LYS LYS ILE LEU HIS ALA GLY PHE LYS SEQRES 9 E 108 MET MET SER LYS SEQRES 1 F 11 SER GLY ARG GLY KCR GLY GLY KCR GLY LEU GLY MODRES 4YYK KCR C 5 LYS MODIFIED RESIDUE MODRES 4YYK KCR C 8 LYS MODIFIED RESIDUE MODRES 4YYK KCR F 5 LYS MODIFIED RESIDUE MODRES 4YYK KCR F 8 LYS MODIFIED RESIDUE HET KCR C 5 14 HET KCR C 8 14 HET KCR F 5 14 HET KCR F 8 14 HETNAM KCR N-6-CROTONYL-L-LYSINE FORMUL 3 KCR 4(C10 H18 N2 O3) FORMUL 7 HOH *95(H2 O) HELIX 1 AA1 THR A 23 LYS A 39 1 17 HELIX 2 AA2 GLY A 56 ILE A 60 5 5 HELIX 3 AA3 ASP A 66 ASN A 77 1 12 HELIX 4 AA4 SER A 81 ASN A 100 1 20 HELIX 5 AA5 THR A 104 MET A 121 1 18 HELIX 6 AA6 THR B 23 ARG B 38 1 16 HELIX 7 AA7 GLY B 56 ILE B 61 1 6 HELIX 8 AA8 ASP B 66 ALA B 76 1 11 HELIX 9 AA9 SER B 81 ASN B 100 1 20 HELIX 10 AB1 THR B 104 MET B 121 1 18 HELIX 11 AB2 THR D 23 ARG D 38 1 16 HELIX 12 AB3 ASP D 66 ALA D 76 1 11 HELIX 13 AB4 SER D 81 ASN D 100 1 20 HELIX 14 AB5 THR D 104 MET D 121 1 18 HELIX 15 AB6 THR E 23 LYS E 39 1 17 HELIX 16 AB7 GLY E 56 ILE E 60 5 5 HELIX 17 AB8 ASP E 66 ALA E 76 1 11 HELIX 18 AB9 SER E 81 ASN E 100 1 20 HELIX 19 AC1 THR E 104 MET E 121 1 18 LINK C GLY C 4 N KCR C 5 1555 1555 1.35 LINK C KCR C 5 N GLY C 6 1555 1555 1.36 LINK C GLY C 7 N KCR C 8 1555 1555 1.34 LINK C KCR C 8 N GLY C 9 1555 1555 1.34 LINK C GLY F 4 N KCR F 5 1555 1555 1.34 LINK C KCR F 5 N GLY F 6 1555 1555 1.35 LINK C GLY F 7 N KCR F 8 1555 1555 1.34 LINK C KCR F 8 N GLY F 9 1555 1555 1.33 CRYST1 24.840 34.730 129.080 89.88 89.81 69.45 P 1 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 0.040258 -0.015092 -0.000119 0.00000 SCALE2 0.000000 0.030750 -0.000031 0.00000 SCALE3 0.000000 0.000000 0.007747 0.00000