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- PDB-3jvj: Crystal structure of the bromodomain 1 in mouse Brd4 -

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Basic information

Entry
Database: PDB / ID: 3jvj
TitleCrystal structure of the bromodomain 1 in mouse Brd4
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN / bromodomain / alpha helical / N-acetyl lysine binding domain / Nucleus / Phosphoprotein
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
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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: Non-polymer description / 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)15,5403
Polymers15,3861
Non-polymers1542
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.014, 47.442, 78.024
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 / Mitotic chromosome-associated protein / MCAP


Mass: 15385.665 Da / Num. of mol.: 1 / Fragment: bromodomain, UNP residues 42-168
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.6M Na formate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2009
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→19.6 Å / Num. all: 18865 / Num. obs: 18865 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.811 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.35
Reflection shellResolution: 1.55→1.6 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 13213 / Num. unique obs: 1668 / % possible all: 99.5

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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 2OSS

2oss


Resolution: 1.55→19.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.61 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 961 5.1 %RANDOM
Rwork0.184 ---
all0.184 18865 --
obs0.186 18855 99.45 %-
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: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.28 Å20 Å20 Å2
2---3.57 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 10 111 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221098
X-RAY DIFFRACTIONr_bond_other_d0.0010.02740
X-RAY DIFFRACTIONr_angle_refined_deg2.2391.9741504
X-RAY DIFFRACTIONr_angle_other_deg1.22731827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16825.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26715184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.272153
X-RAY DIFFRACTIONr_chiral_restr0.1520.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02200
X-RAY DIFFRACTIONr_nbd_refined0.2310.2216
X-RAY DIFFRACTIONr_nbd_other0.1880.2687
X-RAY DIFFRACTIONr_nbtor_refined0.1960.2535
X-RAY DIFFRACTIONr_nbtor_other0.1040.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.210
X-RAY DIFFRACTIONr_mcbond_it2.91.5687
X-RAY DIFFRACTIONr_mcbond_other1.7541.5248
X-RAY DIFFRACTIONr_mcangle_it3.59821081
X-RAY DIFFRACTIONr_scbond_it4.9443495
X-RAY DIFFRACTIONr_scangle_it6.2954.5419
X-RAY DIFFRACTIONr_rigid_bond_restr3.31232104
X-RAY DIFFRACTIONr_sphericity_free14.6723111
X-RAY DIFFRACTIONr_sphericity_bonded9.73731806
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 65 -
Rwork0.239 1274 -
all-1339 -
obs--99.41 %

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