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- PDB-5o38: Human Brd2(BD2) mutant in free form -

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Basic information

Entry
Database: PDB / ID: 5o38
TitleHuman Brd2(BD2) mutant in free form
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / The Bromodomain and Extra-Terminal Domain (BET) Family Chromatin binding protein
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9JB / (2~{S})-1-[(2~{S})-2-oxidanylpropoxy]propan-2-ol / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsChan, K.-H. / Runcie, A.C. / Ciulli, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J001201/2 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/G023123/2 United Kingdom
European Research CouncilERC-2012-StG-311460 DrugE3CRLs
CitationJournal: Chem Sci / Year: 2018
Title: Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition.
Authors: Runcie, A.C. / Zengerle, M. / Chan, K.H. / Testa, A. / van Beurden, L. / Baud, M.G.J. / Epemolu, O. / Ellis, L.C.J. / Read, K.D. / Coulthard, V. / Brien, A. / Ciulli, A.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8414
Polymers13,3611
Non-polymers4803
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 71.409, 31.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-502-

CL

21A-836-

HOH

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Components

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


Mass: 13361.383 Da / Num. of mol.: 1 / Mutation: L383V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P25440
#2: Chemical ChemComp-9JB / 3-[(2~{R})-2-oxidanylpropoxy]-2-[[(2~{R})-2-oxidanylpropoxy]methyl]-2-[[(2~{S})-2-oxidanylpropoxy]methyl]propan-1-ol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DQW / (2~{S})-1-[(2~{S})-2-oxidanylpropoxy]propan-2-ol


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris pH8.0 50% Pentaerythritol propoxylate (5/4 PO/OH) 0.2M Imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.2→19.5 Å / Num. obs: 37657 / % possible obs: 98.26 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02237 / Net I/σ(I): 15.57
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.08386 / Mean I/σ(I) obs: 6.62 / Num. unique obs: 3520 / CC1/2: 0.974 / % possible all: 93.37

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QEU

4qeu


Resolution: 1.2→19.499 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1413 1833 4.87 %
Rwork0.1178 --
obs0.1189 37657 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→19.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 31 237 1198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051055
X-RAY DIFFRACTIONf_angle_d1.031429
X-RAY DIFFRACTIONf_dihedral_angle_d10.751427
X-RAY DIFFRACTIONf_chiral_restr0.076146
X-RAY DIFFRACTIONf_plane_restr0.005182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.23250.12981300.10812551X-RAY DIFFRACTION92
1.2325-1.26870.13831520.09862646X-RAY DIFFRACTION97
1.2687-1.30970.14751520.09822693X-RAY DIFFRACTION98
1.3097-1.35650.13941250.0982730X-RAY DIFFRACTION99
1.3565-1.41080.13991390.09712772X-RAY DIFFRACTION99
1.4108-1.47490.1321180.09652789X-RAY DIFFRACTION99
1.4749-1.55270.12731340.09212739X-RAY DIFFRACTION99
1.5527-1.64990.12221320.09332795X-RAY DIFFRACTION100
1.6499-1.77720.12791580.10412771X-RAY DIFFRACTION100
1.7772-1.95590.14461300.11432804X-RAY DIFFRACTION99
1.9559-2.23860.11331430.11682767X-RAY DIFFRACTION98
2.2386-2.8190.13661400.13942852X-RAY DIFFRACTION100
2.819-19.50120.1721800.14112915X-RAY DIFFRACTION98

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