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- PDB-5o39: Human Brd2(BD2) mutant in complex with ME -

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Basic information

Entry
Database: PDB / ID: 5o39
TitleHuman Brd2(BD2) mutant in complex with ME
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / The Bromodomain and Extra-Terminal Domain (BET) Family Chromatin binding protein
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 II / Brdt, bromodomain, repeat I / 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 II / Brdt, bromodomain, repeat I / 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-31O / (2~{S})-1-[(2~{S})-2-oxidanylpropoxy]propan-2-ol / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRuncie, A.C. / Chan, K.-H. / 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)13,9564
Polymers13,3611
Non-polymers5953
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.406, 72.129, 31.990
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

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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-31O / methyl (2R)-2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]propanoate


Mass: 424.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21ClN4O3
#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.: 203 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 0.2M Tris pH9 53% Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→21.77 Å / Num. obs: 12633 / % possible obs: 97.12 % / Redundancy: 17.1 % / CC1/2: 1 / Rmerge(I) obs: 0.04883 / Net I/σ(I): 43.16
Reflection shellResolution: 1.74→1.802 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.05565 / Num. unique obs: 291 / CC1/2: 0.999 / % possible all: 79.28

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QEU

4qeu


Resolution: 1.74→21.769 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 632 5 %random
Rwork0.1442 ---
obs0.1464 12632 97.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→21.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 40 203 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007988
X-RAY DIFFRACTIONf_angle_d1.0471332
X-RAY DIFFRACTIONf_dihedral_angle_d10.762365
X-RAY DIFFRACTIONf_chiral_restr0.041133
X-RAY DIFFRACTIONf_plane_restr0.004168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.87430.20651130.13992079X-RAY DIFFRACTION86
1.8743-2.06280.18181310.13082401X-RAY DIFFRACTION100
2.0628-2.3610.16871200.14052444X-RAY DIFFRACTION100
2.361-2.97340.18651340.15052481X-RAY DIFFRACTION100
2.9734-21.7710.20181340.14842595X-RAY DIFFRACTION100

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