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- PDB-4j1p: X-ray crystal structure of bromodomain 2 of human brd2 in complex... -

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Basic information

Entry
Database: PDB / ID: 4j1p
TitleX-ray crystal structure of bromodomain 2 of human brd2 in complex with rvx208 to 1.08 A resolution
ComponentsBromodomain containing 2, isoform CRA_a
KeywordsSIGNALING PROTEIN/INHIBITOR / BRD2 / BROMODOMAIN / SIGNALING PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1K0 / Bromodomain-containing protein 2 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.08 Å
AuthorsStein, A.J. / White, A. / Suto, R.K.
CitationJournal: Plos One / Year: 2013
Title: RVX-208, an Inducer of ApoA-I in Humans, Is a BET Bromodomain Antagonist.
Authors: McLure, K.G. / Gesner, E.M. / Tsujikawa, L. / Kharenko, O.A. / Attwell, S. / Campeau, E. / Wasiak, S. / Stein, A. / White, A. / Fontano, E. / Suto, R.K. / Wong, N.C. / Wagner, G.S. / Hansen, H.C. / Young, P.R.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 2, isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8083
Polymers13,3751
Non-polymers4322
Water4,576254
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.100, 66.350, 75.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT MAY BE DIMERIC, BUT PRESENTLY THIS IS UNKNOWN.

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Components

#1: Protein Bromodomain containing 2, isoform CRA_a / Bromodomain-containing protein 2 / Putative uncharacterized protein DKFZp313H139


Mass: 13375.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, DKFZp313H139, hCG_17503 / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q658Y7, UniProt: P25440*PLUS
#2: Chemical ChemComp-1K0 / 2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one


Mass: 370.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O5
#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.: 254 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 25% (w/v) PEG 1500, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. all: 55667 / Num. obs: 55428 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.043 / Χ2: 1.105 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.08-1.124.50.38855060.879199.9
1.12-1.164.50.23255020.8651100
1.16-1.224.50.18754900.973199.9
1.22-1.284.50.14355311.032199.9
1.28-1.364.60.10755170.9681100
1.36-1.474.70.08655391.0051100
1.47-1.614.70.07555671.3691100
1.61-1.854.70.05755571.3711100
1.85-2.334.70.03956271.249199.9
2.33-504.60.0355921.288196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ONI

3oni


Resolution: 1.08→19.56 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.49 / SU B: 0.665 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.028 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1592 2813 5.1 %RANDOM
Rwork0.1279 ---
obs0.1295 55278 99.28 %-
all-55679 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.49 Å2 / Biso mean: 15.8182 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.52 Å2-0 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.08→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 31 254 1223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0191080
X-RAY DIFFRACTIONr_bond_other_d0.0010.021036
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.9931468
X-RAY DIFFRACTIONr_angle_other_deg1.20232406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02723.46252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20415204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.88157
X-RAY DIFFRACTIONr_chiral_restr0.1450.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0211216
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02256
X-RAY DIFFRACTIONr_rigid_bond_restr7.20932112
X-RAY DIFFRACTIONr_sphericity_free28.105529
X-RAY DIFFRACTIONr_sphericity_bonded10.95252302
LS refinement shellResolution: 1.08→1.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 203 -
Rwork0.314 3817 -
all-4020 -
obs--98.43 %

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