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- PDB-7usg: BRD2-BD2 in complex with MDP5 -

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Basic information

Entry
Database: PDB / ID: 7usg
TitleBRD2-BD2 in complex with MDP5
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION/INHIBITOR / Inhibitor / acetyllysine binding pocket / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / 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 ...chromatin looping / acetylation-dependent protein binding / 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 phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-O6O / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJayasinghe, T.D. / Ronning, D.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Control Release / Year: 2023
Title: Targeting BRD4 and PI3K signaling pathways for the treatment of medulloblastoma.
Authors: Sethi, B. / Kumar, V. / Jayasinghe, T.D. / Dong, Y. / Ronning, D.R. / Zhong, H.A. / Coulter, D.W. / Mahato, R.I.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5695
Polymers13,0561
Non-polymers5134
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.560, 72.277, 32.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-504-

NA

21A-818-

HOH

31A-844-

HOH

41A-847-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13056.032 Da / Num. of mol.: 1 / Fragment: BD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-O6O / (8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one


Mass: 365.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 16 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.2→19.6 Å / Num. obs: 35996 / % possible obs: 91.85 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.18 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.039 / Net I/σ(I): 28.7
Reflection shellResolution: 1.2→1.243 Å / Num. unique obs: 3501 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6J

6e6j


Resolution: 1.2→19.6 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 2000 5.56 %
Rwork0.1772 33996 -
obs0.1783 35996 91.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.93 Å2 / Biso mean: 15.0309 Å2 / Biso min: 6.68 Å2
Refinement stepCycle: final / Resolution: 1.2→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 36 247 1198
Biso mean--16.79 23.43 -
Num. residues----111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.230.26811370.25082334247190
1.23-1.260.25961390.24122355249491
1.26-1.30.25971390.22822370250990
1.3-1.340.23671410.21822386252791
1.34-1.390.24071390.212353249291
1.39-1.450.21861390.19922372251191
1.45-1.510.21231410.18722403254491
1.51-1.590.18611420.17542417255993
1.59-1.690.19021460.16712482262894
1.69-1.820.19981470.17932499264695
1.82-20.20251470.17892509265694
2-2.290.18011480.16642496264493
2.29-2.890.19841470.17392512265993
2.89-19.60.17491480.15652508265689

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