HEADER TRANSCRIPTION 01-AUG-06 2DVQ TITLE CRYSTAL STRUCTURE ANALYSIS OF THE N-TERMINAL BROMODOMAIN OF HUMAN BRD2 TITLE 2 COMPLEXED WITH ACETYLATED HISTONE H4 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: N-TERMINAL BROMODOMAIN, BD1; COMPND 5 SYNONYM: RING3 PROTEIN, O27.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H4; COMPND 9 CHAIN: P, Q; COMPND 10 FRAGMENT: N-TERM 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCR2.1-TOPO VECTOR; SOURCE 9 OTHER_DETAILS: EXPRESSED BY CELL-FREE SYSTEM; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS ALPHA-HELICAL DOMAIN, BROMODOMAIN, BINDS TO ACETYLATED HISTONES, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKAMURA,T.UMEHARA,M.SHIROUZU,B.PADMANABHAN,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 03-APR-24 2DVQ 1 SEQADV LINK REVDAT 3 16-MAR-10 2DVQ 1 JRNL REVDAT 2 24-FEB-09 2DVQ 1 VERSN REVDAT 1 07-AUG-07 2DVQ 0 JRNL AUTH T.UMEHARA,Y.NAKAMURA,M.K.JANG,K.NAKANO,A.TANAKA,K.OZATO, JRNL AUTH 2 B.PADMANABHAN,S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR ACETYLATED HISTONE H4 RECOGNITION BY JRNL TITL 2 THE HUMAN BRD2 BROMODOMAIN. JRNL REF J.BIOL.CHEM. V. 285 7610 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20048151 JRNL DOI 10.1074/JBC.M109.062422 REMARK 2 REMARK 2 RESOLUTION. 2.04 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 24375 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1301 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1360 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2911 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.14000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.840 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2987 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4028 ; 1.547 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 351 ; 6.491 ; 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): 423 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2248 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1550 ; 0.237 ; 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): 194 ; 0.168 ; 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): 71 ; 0.266 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.351 ; 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): 1776 ; 1.011 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2860 ; 1.878 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1211 ; 3.304 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1168 ; 4.730 ; 4.500 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 : 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 2DVQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000025901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25699 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06800 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) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 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: BD1 NATIVE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEGMME 5K, AS, PH 6.50, VAPOR REMARK 280 DIFFUSION, CO-CRYSTALLIZAATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.90550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.57150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.90550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.57150 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 -1.000000 0.000000 0.000000 113.81100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 195 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 229 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 257 LIES ON A SPECIAL POSITION. 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 LEU A 187 REMARK 465 VAL A 188 REMARK 465 VAL A 189 REMARK 465 THR A 190 REMARK 465 ILE A 191 REMARK 465 PRO A 192 REMARK 465 LYS A 193 REMARK 465 ASN A 194 REMARK 465 GLN B 185 REMARK 465 GLU B 186 REMARK 465 LEU B 187 REMARK 465 VAL B 188 REMARK 465 VAL B 189 REMARK 465 THR B 190 REMARK 465 ILE B 191 REMARK 465 PRO B 192 REMARK 465 LYS B 193 REMARK 465 ASN B 194 REMARK 465 GLY C 73 REMARK 465 ARG C 74 REMARK 465 VAL C 75 REMARK 465 GLU C 183 REMARK 465 GLU C 184 REMARK 465 GLN C 185 REMARK 465 GLU C 186 REMARK 465 LEU C 187 REMARK 465 VAL C 188 REMARK 465 VAL C 189 REMARK 465 THR C 190 REMARK 465 ILE C 191 REMARK 465 PRO C 192 REMARK 465 LYS C 193 REMARK 465 ASN C 194 REMARK 465 SER P 1 REMARK 465 GLY P 2 REMARK 465 ARG P 3 REMARK 465 GLY P 4 REMARK 465 LYS P 5 REMARK 465 GLY P 6 REMARK 465 GLY P 7 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 P 8 CG CD CE NZ REMARK 470 ARG Q 3 CG CD NE CZ NH1 NH2 REMARK 470 LYS Q 5 CG CD CE NZ 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 C 208 O HOH C 208 2655 1.90 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 A 160 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 GLY Q 7 N - CA - C ANGL. DEV. = -16.2 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 GLU A 184 93.17 -57.63 REMARK 500 VAL B 75 113.29 69.35 REMARK 500 LEU B 110 68.21 -118.43 REMARK 500 LEU C 110 67.60 -116.05 REMARK 500 LEU P 10 -39.62 -141.87 REMARK 500 ARG Q 3 -52.88 -141.21 REMARK 500 LYS Q 8 93.03 -174.32 REMARK 500 LEU Q 10 -40.43 -175.85 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 -143.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X0J RELATED DB: PDB REMARK 900 NATIVE REMARK 900 RELATED ID: 2DVR RELATED DB: PDB REMARK 900 RELATED ID: 2DVS RELATED DB: PDB REMARK 900 RELATED ID: AR_001000221.4 RELATED DB: TARGETDB DBREF 2DVQ A 73 194 UNP P25440 BRD2_HUMAN 73 194 DBREF 2DVQ B 73 194 UNP P25440 BRD2_HUMAN 73 194 DBREF 2DVQ C 73 194 UNP P25440 BRD2_HUMAN 73 194 DBREF 2DVQ P 1 15 PDB 2DVQ 2DVQ 1 15 DBREF 2DVQ Q 1 15 PDB 2DVQ 2DVQ 1 15 SEQADV 2DVQ MSE A 87 UNP P25440 MET 87 MODIFIED RESIDUE SEQADV 2DVQ MSE A 121 UNP P25440 MET 121 MODIFIED RESIDUE SEQADV 2DVQ MSE A 123 UNP P25440 MET 123 MODIFIED RESIDUE SEQADV 2DVQ MSE A 142 UNP P25440 MET 142 MODIFIED RESIDUE SEQADV 2DVQ MSE A 148 UNP P25440 MET 148 MODIFIED RESIDUE SEQADV 2DVQ MSE A 165 UNP P25440 MET 165 MODIFIED RESIDUE SEQADV 2DVQ MSE A 180 UNP P25440 MET 180 MODIFIED RESIDUE SEQADV 2DVQ MSE B 87 UNP P25440 MET 87 MODIFIED RESIDUE SEQADV 2DVQ MSE B 121 UNP P25440 MET 121 MODIFIED RESIDUE SEQADV 2DVQ MSE B 123 UNP P25440 MET 123 MODIFIED RESIDUE SEQADV 2DVQ MSE B 142 UNP P25440 MET 142 MODIFIED RESIDUE SEQADV 2DVQ MSE B 148 UNP P25440 MET 148 MODIFIED RESIDUE SEQADV 2DVQ MSE B 165 UNP P25440 MET 165 MODIFIED RESIDUE SEQADV 2DVQ MSE B 180 UNP P25440 MET 180 MODIFIED RESIDUE SEQADV 2DVQ MSE C 87 UNP P25440 MET 87 MODIFIED RESIDUE SEQADV 2DVQ MSE C 121 UNP P25440 MET 121 MODIFIED RESIDUE SEQADV 2DVQ MSE C 123 UNP P25440 MET 123 MODIFIED RESIDUE SEQADV 2DVQ MSE C 142 UNP P25440 MET 142 MODIFIED RESIDUE SEQADV 2DVQ MSE C 148 UNP P25440 MET 148 MODIFIED RESIDUE SEQADV 2DVQ MSE C 165 UNP P25440 MET 165 MODIFIED RESIDUE SEQADV 2DVQ MSE C 180 UNP P25440 MET 180 MODIFIED RESIDUE SEQRES 1 A 122 GLY ARG VAL THR ASN GLN LEU GLN TYR LEU HIS LYS VAL SEQRES 2 A 122 VAL MSE LYS ALA LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 3 A 122 PHE ARG GLN PRO VAL ASP ALA VAL LYS LEU GLY LEU PRO SEQRES 4 A 122 ASP TYR HIS LYS ILE ILE LYS GLN PRO MSE ASP MSE GLY SEQRES 5 A 122 THR ILE LYS ARG ARG LEU GLU ASN ASN TYR TYR TRP ALA SEQRES 6 A 122 ALA SER GLU CYS MSE GLN ASP PHE ASN THR MSE PHE THR SEQRES 7 A 122 ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL SEQRES 8 A 122 LEU MSE ALA GLN THR LEU GLU LYS ILE PHE LEU GLN LYS SEQRES 9 A 122 VAL ALA SER MSE PRO GLN GLU GLU GLN GLU LEU VAL VAL SEQRES 10 A 122 THR ILE PRO LYS ASN SEQRES 1 B 122 GLY ARG VAL THR ASN GLN LEU GLN TYR LEU HIS LYS VAL SEQRES 2 B 122 VAL MSE LYS ALA LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 3 B 122 PHE ARG GLN PRO VAL ASP ALA VAL LYS LEU GLY LEU PRO SEQRES 4 B 122 ASP TYR HIS LYS ILE ILE LYS GLN PRO MSE ASP MSE GLY SEQRES 5 B 122 THR ILE LYS ARG ARG LEU GLU ASN ASN TYR TYR TRP ALA SEQRES 6 B 122 ALA SER GLU CYS MSE GLN ASP PHE ASN THR MSE PHE THR SEQRES 7 B 122 ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL SEQRES 8 B 122 LEU MSE ALA GLN THR LEU GLU LYS ILE PHE LEU GLN LYS SEQRES 9 B 122 VAL ALA SER MSE PRO GLN GLU GLU GLN GLU LEU VAL VAL SEQRES 10 B 122 THR ILE PRO LYS ASN SEQRES 1 C 122 GLY ARG VAL THR ASN GLN LEU GLN TYR LEU HIS LYS VAL SEQRES 2 C 122 VAL MSE LYS ALA LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 3 C 122 PHE ARG GLN PRO VAL ASP ALA VAL LYS LEU GLY LEU PRO SEQRES 4 C 122 ASP TYR HIS LYS ILE ILE LYS GLN PRO MSE ASP MSE GLY SEQRES 5 C 122 THR ILE LYS ARG ARG LEU GLU ASN ASN TYR TYR TRP ALA SEQRES 6 C 122 ALA SER GLU CYS MSE GLN ASP PHE ASN THR MSE PHE THR SEQRES 7 C 122 ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL SEQRES 8 C 122 LEU MSE ALA GLN THR LEU GLU LYS ILE PHE LEU GLN LYS SEQRES 9 C 122 VAL ALA SER MSE PRO GLN GLU GLU GLN GLU LEU VAL VAL SEQRES 10 C 122 THR ILE PRO LYS ASN SEQRES 1 P 15 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY ALY GLY SEQRES 2 P 15 GLY ALA SEQRES 1 Q 15 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY ALY GLY SEQRES 2 Q 15 GLY ALA MODRES 2DVQ MSE A 87 MET SELENOMETHIONINE MODRES 2DVQ MSE A 121 MET SELENOMETHIONINE MODRES 2DVQ MSE A 123 MET SELENOMETHIONINE MODRES 2DVQ MSE A 142 MET SELENOMETHIONINE MODRES 2DVQ MSE A 148 MET SELENOMETHIONINE MODRES 2DVQ MSE A 165 MET SELENOMETHIONINE MODRES 2DVQ MSE A 180 MET SELENOMETHIONINE MODRES 2DVQ MSE B 87 MET SELENOMETHIONINE MODRES 2DVQ MSE B 121 MET SELENOMETHIONINE MODRES 2DVQ MSE B 123 MET SELENOMETHIONINE MODRES 2DVQ MSE B 142 MET SELENOMETHIONINE MODRES 2DVQ MSE B 148 MET SELENOMETHIONINE MODRES 2DVQ MSE B 165 MET SELENOMETHIONINE MODRES 2DVQ MSE B 180 MET SELENOMETHIONINE MODRES 2DVQ MSE C 87 MET SELENOMETHIONINE MODRES 2DVQ MSE C 121 MET SELENOMETHIONINE MODRES 2DVQ MSE C 123 MET SELENOMETHIONINE MODRES 2DVQ MSE C 142 MET SELENOMETHIONINE MODRES 2DVQ MSE C 148 MET SELENOMETHIONINE MODRES 2DVQ MSE C 165 MET SELENOMETHIONINE MODRES 2DVQ MSE C 180 MET SELENOMETHIONINE MODRES 2DVQ ALY P 12 LYS N(6)-ACETYLLYSINE MODRES 2DVQ ALY Q 12 LYS N(6)-ACETYLLYSINE HET MSE A 87 8 HET MSE A 121 8 HET MSE A 123 8 HET MSE A 142 8 HET MSE A 148 8 HET MSE A 165 8 HET MSE A 180 8 HET MSE B 87 8 HET MSE B 121 8 HET MSE B 123 8 HET MSE B 142 8 HET MSE B 148 8 HET MSE B 165 8 HET MSE B 180 8 HET MSE C 87 8 HET MSE C 121 8 HET MSE C 123 8 HET MSE C 142 8 HET MSE C 148 8 HET MSE C 165 8 HET MSE C 180 8 HET ALY P 12 12 HET ALY Q 12 12 HETNAM MSE SELENOMETHIONINE HETNAM ALY N(6)-ACETYLLYSINE FORMUL 1 MSE 21(C5 H11 N O2 SE) FORMUL 4 ALY 2(C8 H16 N2 O3) FORMUL 6 HOH *250(H2 O) HELIX 1 1 THR A 76 VAL A 85 1 10 HELIX 2 2 VAL A 85 LYS A 92 1 8 HELIX 3 3 ALA A 96 ARG A 100 5 5 HELIX 4 4 ASP A 104 GLY A 109 1 6 HELIX 5 5 ASP A 112 ILE A 117 1 6 HELIX 6 6 ASP A 122 ASN A 132 1 11 HELIX 7 7 ALA A 137 ASN A 156 1 20 HELIX 8 8 ASP A 160 SER A 179 1 20 HELIX 9 9 THR B 76 VAL B 85 1 10 HELIX 10 10 VAL B 85 LYS B 92 1 8 HELIX 11 11 ALA B 96 ARG B 100 5 5 HELIX 12 12 ASP B 104 GLY B 109 1 6 HELIX 13 13 ASP B 112 ILE B 117 1 6 HELIX 14 14 ASP B 122 ASN B 132 1 11 HELIX 15 15 ALA B 137 ASN B 156 1 20 HELIX 16 16 ASP B 160 ALA B 178 1 19 HELIX 17 17 THR C 76 VAL C 85 1 10 HELIX 18 18 VAL C 85 HIS C 93 1 9 HELIX 19 19 GLN C 94 ARG C 100 5 7 HELIX 20 20 ASP C 112 ILE C 117 1 6 HELIX 21 21 ASP C 122 ASN C 132 1 11 HELIX 22 22 ALA C 137 ASN C 156 1 20 HELIX 23 23 ASP C 160 SER C 179 1 20 LINK C VAL A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N LYS A 88 1555 1555 1.34 LINK C PRO A 120 N MSE A 121 1555 1555 1.33 LINK C MSE A 121 N ASP A 122 1555 1555 1.33 LINK C ASP A 122 N MSE A 123 1555 1555 1.33 LINK C MSE A 123 N GLY A 124 1555 1555 1.33 LINK C CYS A 141 N MSE A 142 1555 1555 1.32 LINK C MSE A 142 N GLN A 143 1555 1555 1.33 LINK C THR A 147 N MSE A 148 1555 1555 1.34 LINK C MSE A 148 N PHE A 149 1555 1555 1.33 LINK C LEU A 164 N MSE A 165 1555 1555 1.31 LINK C MSE A 165 N ALA A 166 1555 1555 1.33 LINK C SER A 179 N MSE A 180 1555 1555 1.33 LINK C MSE A 180 N PRO A 181 1555 1555 1.34 LINK C VAL B 86 N MSE B 87 1555 1555 1.33 LINK C MSE B 87 N LYS B 88 1555 1555 1.33 LINK C PRO B 120 N MSE B 121 1555 1555 1.33 LINK C MSE B 121 N ASP B 122 1555 1555 1.33 LINK C ASP B 122 N MSE B 123 1555 1555 1.35 LINK C MSE B 123 N GLY B 124 1555 1555 1.33 LINK C CYS B 141 N MSE B 142 1555 1555 1.32 LINK C MSE B 142 N GLN B 143 1555 1555 1.33 LINK C THR B 147 N MSE B 148 1555 1555 1.33 LINK C MSE B 148 N PHE B 149 1555 1555 1.34 LINK C LEU B 164 N MSE B 165 1555 1555 1.33 LINK C MSE B 165 N ALA B 166 1555 1555 1.34 LINK C SER B 179 N MSE B 180 1555 1555 1.32 LINK C MSE B 180 N PRO B 181 1555 1555 1.34 LINK C VAL C 86 N MSE C 87 1555 1555 1.34 LINK C MSE C 87 N LYS C 88 1555 1555 1.34 LINK C PRO C 120 N MSE C 121 1555 1555 1.33 LINK C MSE C 121 N ASP C 122 1555 1555 1.32 LINK C ASP C 122 N MSE C 123 1555 1555 1.34 LINK C MSE C 123 N GLY C 124 1555 1555 1.33 LINK C CYS C 141 N MSE C 142 1555 1555 1.32 LINK C MSE C 142 N GLN C 143 1555 1555 1.33 LINK C THR C 147 N MSE C 148 1555 1555 1.32 LINK C MSE C 148 N PHE C 149 1555 1555 1.33 LINK C LEU C 164 N MSE C 165 1555 1555 1.33 LINK C MSE C 165 N ALA C 166 1555 1555 1.34 LINK C SER C 179 N MSE C 180 1555 1555 1.32 LINK C MSE C 180 N PRO C 181 1555 1555 1.34 LINK C GLY P 11 N ALY P 12 1555 1555 1.32 LINK C ALY P 12 N GLY P 13 1555 1555 1.33 LINK C GLY Q 11 N ALY Q 12 1555 1555 1.33 LINK C ALY Q 12 N GLY Q 13 1555 1555 1.34 CISPEP 1 GLY P 14 ALA P 15 0 3.37 CISPEP 2 SER Q 1 GLY Q 2 0 -14.85 CRYST1 113.811 55.143 67.489 90.00 94.06 90.00 C 1 2 1 12 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 0.008786 0.000000 0.000624 0.00000 SCALE2 0.000000 0.018135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014855 0.00000