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- PDB-4qev: Crystal structure of BRD2(BD2) mutant with ligand ME bound (METHY... -

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Basic information

Entry
Database: PDB / ID: 4qev
TitleCrystal structure of BRD2(BD2) mutant with ligand ME bound (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)
ComponentsBromodomain-containing protein 2
Keywordstranscription/transcription inhibitor / Bromodomain-containing protein 2 / KIAA9001 / RING3 / Transcription regulation / transcription-transcription 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 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 / NICKEL (II) ION / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTallant, C. / Baud, M. / Lin-Shiao, E. / Chirgadze, D.Y. / Ciulli, A.
CitationJournal: Science / Year: 2014
Title: Chemical biology. A bump-and-hole approach to engineer controlled selectivity of BET bromodomain chemical probes.
Authors: Baud, M.G. / Lin-Shiao, E. / Cardote, T. / Tallant, C. / Pschibul, A. / Chan, K.H. / Zengerle, M. / Garcia, J.R. / Kwan, T.T. / Ferguson, F.M. / Ciulli, A.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Sep 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
Revision 1.3Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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)14,3235
Polymers13,3331
Non-polymers9904
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bromodomain-containing protein 2
hetero molecules

A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,64710
Polymers26,6672
Non-polymers1,9808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3170 Å2
ΔGint-13 kcal/mol
Surface area11960 Å2
MethodPISA
3
A: Bromodomain-containing protein 2
hetero molecules

A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,64710
Polymers26,6672
Non-polymers1,9808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area2970 Å2
ΔGint-1 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.516, 71.468, 32.067
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-503-

NI

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13333.330 Da / Num. of mol.: 1 / Fragment: unp residues 344-455 / Mutation: L383A
Source method: isolated from a genetically manipulated source
Details: LIC cloning / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pNIC28-Bsa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P25440

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Non-polymers , 5 types, 73 molecules

#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-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes, 0.2M Imidazole, 41% PEG400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32.1 Å / Num. all: 11758 / Num. obs: 11157 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.1 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
1.8-1.833.720.46193.065660.2843
1.9-1.944.530.33573.915670.2442
2.03-2.084.990.21835.545510.1745
2.21-2.285.540.15588.045830.1142
2.58-2.727.390.11813.715900.0634
3.47-49.380.089523.755880.0389
7.86-328.760.062226.981780.0383

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0029refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2DVV

2dvv


Resolution: 1.8→32.07 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.542 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22614 557 4.8 %RANDOM
Rwork0.18715 ---
obs0.18902 11157 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.444 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 59 69 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191006
X-RAY DIFFRACTIONr_bond_other_d0.0020.02947
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0071352
X-RAY DIFFRACTIONr_angle_other_deg0.7693.0062187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.925113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39623.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27715169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.431157
X-RAY DIFFRACTIONr_chiral_restr0.070.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211099
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 35 -
Rwork0.273 765 -
obs--95.01 %
Refinement TLS params.Method: refined / Origin x: 62.5781 Å / Origin y: 2.8319 Å / Origin z: 64.935 Å
111213212223313233
T0.0008 Å20 Å2-0.0027 Å2-0.0014 Å2-0.0008 Å2--0.0443 Å2
L0.3721 °2-0.1065 °20.0518 °2-0.8665 °2-0.1488 °2--0.0871 °2
S0.0044 Å °-0.009 Å °0.0087 Å °-0.0098 Å °0.0115 Å °-0.0149 Å °0.0076 Å °0.0023 Å °-0.0159 Å °

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