HEADER TRANSCRIPTION 27-NOV-06 2E3K TITLE CRYSTAL STRUCTURE OF THE HUMAN BRD2 SECOND BROMODOMAIN IN COMPLEXED TITLE 2 WITH THE ACETYLATED HISTONE H4 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: THE SECOND BROMODOMAIN, BD2, RESIDUES 348-455; COMPND 5 SYNONYM: PROTEIN RING3, O27.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 15-MER PEPTIDE FROM HISTONE H4; COMPND 9 CHAIN: Q, R; COMPND 10 FRAGMENT: N-TERMINAL H4 DI-ACETYLATED TAIL; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC PEPTIDE. THE SEQUENCE OF THE PEPTIDE IS SOURCE 13 NATURALLY FOUND IN OTHER SOURCE ORGANISM IN ADDITION TO BAKER'S SOURCE 14 YEAST REFERED IN DBREF RECORD. KEYWDS BROMODOMAIN, BINDS TO ACETYLATED HISTONE TAILS, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 15-NOV-23 2E3K 1 REMARK REVDAT 3 25-OCT-23 2E3K 1 SEQADV LINK REVDAT 2 24-FEB-09 2E3K 1 VERSN REVDAT 1 11-DEC-07 2E3K 0 JRNL AUTH B.PADMANABHAN,T.UMEHARA,K.NAKANO,M.K.JANG,K.OZATO,S.YOKOHAMA JRNL TITL STRUCTURAL BASIS FOR DIACETYLATED HISTONE H4 TAIL JRNL TITL 2 RECOGNITION BY THE SECOND BROMODOMAIN OF HUMAN BRD2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 21151 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1144 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1548 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.78000 REMARK 3 B22 (A**2) : -0.85000 REMARK 3 B33 (A**2) : -0.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.459 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.201 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.036 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3864 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5189 ; 1.871 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 457 ; 5.940 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2969 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2035 ; 0.246 ; 0.200 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): 253 ; 0.196 ; 0.200 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): 78 ; 0.259 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.264 ; 0.200 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): 2316 ; 1.489 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3681 ; 2.424 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1548 ; 2.753 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1508 ; 3.728 ; 4.000 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 350 A 455 5 REMARK 3 1 C 350 C 455 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 424 ; 0.29 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 452 ; 0.72 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 424 ; 1.75 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 452 ; 2.92 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 350 B 455 5 REMARK 3 1 D 350 D 455 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 424 ; 0.35 ; 0.50 REMARK 3 LOOSE POSITIONAL 2 B (A): 452 ; 0.89 ; 5.00 REMARK 3 MEDIUM THERMAL 2 B (A**2): 424 ; 1.88 ; 2.00 REMARK 3 LOOSE THERMAL 2 B (A**2): 452 ; 2.63 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2E3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000026180. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22434 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.16600 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: MOLREP REMARK 200 STARTING MODEL: 2DVV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM ACETATE,, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 64.29550 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 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, C, Q 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: B, D, R 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 344 REMARK 465 SER A 345 REMARK 465 HIS A 346 REMARK 465 MET A 347 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLY C 344 REMARK 465 SER C 345 REMARK 465 HIS C 346 REMARK 465 MET C 347 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 HIS D 1 REMARK 465 SER R 1 REMARK 465 GLY R 2 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 GLU A 348 CG CD OE1 OE2 REMARK 470 ASP A 455 CG OD1 OD2 REMARK 470 HIS B 1 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 455 CG OD1 OD2 REMARK 470 ASP C 455 CG OD1 OD2 REMARK 470 MET D 2 CG SD CE REMARK 470 ASP D 455 CG OD1 OD2 REMARK 470 ARG R 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 OD2 ASP A 444 O HOH A 456 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 A 542 O HOH B 462 1554 2.00 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 388 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 434 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP C 388 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP C 395 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 407 CB - CG - OD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP D 407 CB - CG - OD2 ANGL. DEV. = 5.6 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 GLN A 349 -42.61 -16.17 REMARK 500 ALA A 366 -35.19 -38.51 REMARK 500 LEU A 383 76.33 -110.45 REMARK 500 LYS B 364 -40.00 -33.66 REMARK 500 ALA B 380 43.36 -72.94 REMARK 500 LEU B 381 3.07 -166.41 REMARK 500 LEU B 383 58.96 -100.77 REMARK 500 ARG D 406 27.19 47.38 REMARK 500 LEU R 10 -88.81 165.67 REMARK 500 ALY R 12 91.96 -58.61 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 GLY Q 2 ARG Q 3 -134.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DVV RELATED DB: PDB REMARK 900 NATIVE STRUCTURE REMARK 900 RELATED ID: HSO003006073.1 RELATED DB: TARGETDB DBREF 2E3K A 348 455 UNP P25440 BRD2_HUMAN 348 455 DBREF 2E3K B 348 455 UNP P25440 BRD2_HUMAN 348 455 DBREF 2E3K C 348 455 UNP P25440 BRD2_HUMAN 348 455 DBREF 2E3K D 348 455 UNP P25440 BRD2_HUMAN 348 455 DBREF 2E3K Q 1 15 UNP P02309 H4_YEAST 1 15 DBREF 2E3K R 1 15 UNP P02309 H4_YEAST 1 15 SEQADV 2E3K GLY A 344 UNP P25440 EXPRESSION TAG SEQADV 2E3K SER A 345 UNP P25440 EXPRESSION TAG SEQADV 2E3K HIS A 346 UNP P25440 EXPRESSION TAG SEQADV 2E3K MET A 347 UNP P25440 EXPRESSION TAG SEQADV 2E3K GLY B -1 UNP P25440 EXPRESSION TAG SEQADV 2E3K SER B 0 UNP P25440 EXPRESSION TAG SEQADV 2E3K HIS B 1 UNP P25440 EXPRESSION TAG SEQADV 2E3K MET B 2 UNP P25440 EXPRESSION TAG SEQADV 2E3K GLY C 344 UNP P25440 EXPRESSION TAG SEQADV 2E3K SER C 345 UNP P25440 EXPRESSION TAG SEQADV 2E3K HIS C 346 UNP P25440 EXPRESSION TAG SEQADV 2E3K MET C 347 UNP P25440 EXPRESSION TAG SEQADV 2E3K GLY D -1 UNP P25440 EXPRESSION TAG SEQADV 2E3K SER D 0 UNP P25440 EXPRESSION TAG SEQADV 2E3K HIS D 1 UNP P25440 EXPRESSION TAG SEQADV 2E3K MET D 2 UNP P25440 EXPRESSION TAG SEQRES 1 A 112 GLY SER HIS MET GLU GLN LEU LYS HIS CYS ASN GLY ILE SEQRES 2 A 112 LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA SEQRES 3 A 112 TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY SEQRES 4 A 112 LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP SEQRES 5 A 112 LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR SEQRES 6 A 112 ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET SEQRES 7 A 112 PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP SEQRES 8 A 112 VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU SEQRES 9 A 112 PHE ARG TYR ALA LYS MET PRO ASP SEQRES 1 B 112 GLY SER HIS MET GLU GLN LEU LYS HIS CYS ASN GLY ILE SEQRES 2 B 112 LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA SEQRES 3 B 112 TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY SEQRES 4 B 112 LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP SEQRES 5 B 112 LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR SEQRES 6 B 112 ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET SEQRES 7 B 112 PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP SEQRES 8 B 112 VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU SEQRES 9 B 112 PHE ARG TYR ALA LYS MET PRO ASP SEQRES 1 C 112 GLY SER HIS MET GLU GLN LEU LYS HIS CYS ASN GLY ILE SEQRES 2 C 112 LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA SEQRES 3 C 112 TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY SEQRES 4 C 112 LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP SEQRES 5 C 112 LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR SEQRES 6 C 112 ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET SEQRES 7 C 112 PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP SEQRES 8 C 112 VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU SEQRES 9 C 112 PHE ARG TYR ALA LYS MET PRO ASP SEQRES 1 D 112 GLY SER HIS MET GLU GLN LEU LYS HIS CYS ASN GLY ILE SEQRES 2 D 112 LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA SEQRES 3 D 112 TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY SEQRES 4 D 112 LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP SEQRES 5 D 112 LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR SEQRES 6 D 112 ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET SEQRES 7 D 112 PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP SEQRES 8 D 112 VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU SEQRES 9 D 112 PHE ARG TYR ALA LYS MET PRO ASP SEQRES 1 Q 15 SER GLY ARG GLY ALY GLY GLY LYS GLY LEU GLY ALY GLY SEQRES 2 Q 15 GLY ALA SEQRES 1 R 15 SER GLY ARG GLY ALY GLY GLY LYS GLY LEU GLY ALY GLY SEQRES 2 R 15 GLY ALA MODRES 2E3K ALY Q 5 LYS N(6)-ACETYLLYSINE MODRES 2E3K ALY Q 12 LYS N(6)-ACETYLLYSINE MODRES 2E3K ALY R 5 LYS N(6)-ACETYLLYSINE MODRES 2E3K ALY R 12 LYS N(6)-ACETYLLYSINE HET ALY Q 5 12 HET ALY Q 12 12 HET ALY R 5 12 HET ALY R 12 12 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 5 ALY 4(C8 H16 N2 O3) FORMUL 7 HOH *412(H2 O) HELIX 1 1 GLU A 348 SER A 362 1 15 HELIX 2 2 HIS A 365 TRP A 370 1 6 HELIX 3 3 PRO A 371 TYR A 373 5 3 HELIX 4 4 ASP A 377 GLY A 382 1 6 HELIX 5 5 ASP A 385 ILE A 390 1 6 HELIX 6 6 ASP A 395 ASN A 405 1 11 HELIX 7 7 ASP A 410 ASN A 429 1 20 HELIX 8 8 HIS A 433 LYS A 452 1 20 HELIX 9 9 MET B 2 LEU B 361 1 15 HELIX 10 10 SER B 362 LYS B 364 5 3 HELIX 11 11 HIS B 365 TRP B 370 1 6 HELIX 12 12 PRO B 371 TYR B 373 5 3 HELIX 13 13 ALA B 378 GLY B 382 5 5 HELIX 14 14 ASP B 385 ILE B 390 1 6 HELIX 15 15 ASP B 395 ASN B 405 1 11 HELIX 16 16 ASP B 410 ASN B 429 1 20 HELIX 17 17 HIS B 433 LYS B 452 1 20 HELIX 18 18 GLN C 349 SER C 362 1 14 HELIX 19 19 HIS C 365 TRP C 370 1 6 HELIX 20 20 PRO C 371 TYR C 373 5 3 HELIX 21 21 ASP C 377 GLY C 382 1 6 HELIX 22 22 ASP C 385 ILE C 390 1 6 HELIX 23 23 ASP C 395 ASN C 405 1 11 HELIX 24 24 ASP C 410 ASN C 429 1 20 HELIX 25 25 HIS C 433 LYS C 452 1 20 HELIX 26 26 MET D 2 SER D 362 1 16 HELIX 27 27 HIS D 365 TRP D 370 1 6 HELIX 28 28 PRO D 371 TYR D 373 5 3 HELIX 29 29 ASP D 377 GLY D 382 1 6 HELIX 30 30 ASP D 385 ILE D 390 1 6 HELIX 31 31 ASP D 395 ASN D 405 1 11 HELIX 32 32 ASP D 410 ASN D 429 1 20 HELIX 33 33 HIS D 433 LYS D 452 1 20 LINK C GLY Q 4 N ALY Q 5 1555 1555 1.33 LINK C ALY Q 5 N GLY Q 6 1555 1555 1.30 LINK C GLY Q 11 N ALY Q 12 1555 1555 1.32 LINK C ALY Q 12 N GLY Q 13 1555 1555 1.32 LINK C GLY R 4 N ALY R 5 1555 1555 1.34 LINK C ALY R 5 N GLY R 6 1555 1555 1.34 LINK C GLY R 11 N ALY R 12 1555 1555 1.34 LINK C ALY R 12 N GLY R 13 1555 1555 1.32 CRYST1 45.828 128.591 45.847 90.00 104.70 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 0.021821 0.000000 0.005724 0.00000 SCALE2 0.000000 0.007777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022550 0.00000