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- PDB-3jvl: Crystal structure of bromodomain 2 of mouse Brd4 -

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Basic information

Entry
Database: PDB / ID: 3jvl
TitleCrystal structure of bromodomain 2 of mouse Brd4
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN / bromodomain / alpha helical / N-acetyl lysine binding domain
Function / homology
Function and homology information


GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / inner cell mass cell proliferation / RNA polymerase II C-terminal domain binding / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / chromosome segregation / positive regulation of transcription elongation by RNA polymerase II ...GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / inner cell mass cell proliferation / RNA polymerase II C-terminal domain binding / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / chromosome segregation / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsVollmuth, F. / Blankenfeldt, W. / Geyer, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structures of the Dual Bromodomains of the P-TEFb-activating Protein Brd4 at Atomic Resolution
Authors: Vollmuth, F. / Blankenfeldt, W. / Geyer, M.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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)14,2396
Polymers13,8961
Non-polymers3425
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.060, 73.050, 32.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 4 / Mitotic chromosome-associated protein / MCAP


Mass: 13896.040 Da / Num. of mol.: 1 / Fragment: bromodomain 2, UNP residues 349-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brd4 / Plasmid: pProEx-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ESU6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris/HCl, 25% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97642 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2008
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97642 Å / Relative weight: 1
ReflectionResolution: 1.2→19.53 Å / Num. all: 39272 / Num. obs: 39272 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.483 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.37
Reflection shellResolution: 1.2→1.25 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4 / Num. measured obs: 20535 / Num. unique obs: 4460 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OUO

2ouo


Resolution: 1.2→19.53 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.918 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.145 1927 4.9 %RANDOM
Rwork0.116 ---
all0.118 39262 --
obs0.117 39262 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.389 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 24 219 1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0221043
X-RAY DIFFRACTIONr_bond_other_d0.0030.02767
X-RAY DIFFRACTIONr_angle_refined_deg2.5511.9811407
X-RAY DIFFRACTIONr_angle_other_deg1.24831879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97323.40944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17515199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.468156
X-RAY DIFFRACTIONr_chiral_restr0.1560.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021154
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02215
X-RAY DIFFRACTIONr_nbd_refined0.3220.2270
X-RAY DIFFRACTIONr_nbd_other0.2110.2771
X-RAY DIFFRACTIONr_nbtor_refined0.2060.2517
X-RAY DIFFRACTIONr_nbtor_other0.1040.2482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3680.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.229
X-RAY DIFFRACTIONr_mcbond_it2.9211.5681
X-RAY DIFFRACTIONr_mcbond_other1.5171.5246
X-RAY DIFFRACTIONr_mcangle_it3.43621017
X-RAY DIFFRACTIONr_scbond_it5.1213464
X-RAY DIFFRACTIONr_scangle_it6.3044.5377
X-RAY DIFFRACTIONr_rigid_bond_restr3.07432057
X-RAY DIFFRACTIONr_sphericity_free18.7743219
X-RAY DIFFRACTIONr_sphericity_bonded8.94631779
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 123 -
Rwork0.153 2703 -
all-2826 -
obs--100 %

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