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- PDB-2oss: Crystal structure of the Bromo domain 1 in human Bromodomain Cont... -

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Basic information

Entry
Database: PDB / ID: 2oss
TitleCrystal structure of the Bromo domain 1 in human Bromodomain Containing Protein 4 (BRD4)
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN / BRD4 / bromodomain containing protein 4 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFilippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. ...Filippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2864
Polymers15,0991
Non-polymers1863
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.418, 44.139, 78.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / HUNK1 protein


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: Bromo domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3 / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaNO3, 20% PEG3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 8.1 % / Av σ(I) over netI: 14.1 / Number: 237706 / Rmerge(I) obs: 0.071 / Χ2: 1.01 / D res high: 1.35 Å / D res low: 50 Å / Num. obs: 29320 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.915010010.0661.00113.3
2.312.9110010.0841.02610.6
2.022.3199.810.0691.0077.5
1.832.0299.710.0551.037
1.71.8399.910.0641.0027.1
1.61.710010.0781.0197.1
1.521.610010.0961.0077.2
1.451.5210010.1181.0127.2
1.41.4510010.1461.0257.1
1.351.410010.1771.0386.5
ReflectionResolution: 1.35→50 Å / Num. all: 29349 / Num. obs: 29320 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Χ2: 1.015 / Net I/σ(I): 14.1
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.177 / Num. unique all: 2874 / Χ2: 1.038 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å44.14 Å
Translation3.5 Å44.14 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X0J

1x0j


Resolution: 1.35→39.19 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.361 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1485 5.1 %RANDOM
Rwork0.149 ---
all0.15 29280 --
obs0.15 29262 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 12 222 1281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221153
X-RAY DIFFRACTIONr_bond_other_d0.0010.02800
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9831579
X-RAY DIFFRACTIONr_angle_other_deg0.9093.0021964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4975145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63325.84953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63315209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.232153
X-RAY DIFFRACTIONr_chiral_restr0.0760.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined0.2190.2259
X-RAY DIFFRACTIONr_nbd_other0.1710.2788
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2564
X-RAY DIFFRACTIONr_nbtor_other0.090.2522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.226
X-RAY DIFFRACTIONr_mcbond_it1.1121.5732
X-RAY DIFFRACTIONr_mcbond_other0.3541.5255
X-RAY DIFFRACTIONr_mcangle_it1.52821132
X-RAY DIFFRACTIONr_scbond_it2.0913524
X-RAY DIFFRACTIONr_scangle_it2.9034.5438
X-RAY DIFFRACTIONr_rigid_bond_restr1.14432240
X-RAY DIFFRACTIONr_sphericity_free3.783226
X-RAY DIFFRACTIONr_sphericity_bonded2.04631917
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.163 106 -
Rwork0.133 2036 -
obs-2142 99.91 %

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