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- PDB-4yy4: Crystal structure of BRD9 Bromodomain bound to DMSO -

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Basic information

Entry
Database: PDB / ID: 4yy4
TitleCrystal structure of BRD9 Bromodomain bound to DMSO
ComponentsBromodomain-containing protein 9
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsTang, Y. / Bellon, S. / Cochran, A.G. / Poy, F.
CitationJournal: Structure / Year: 2015
Title: A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications.
Authors: Flynn, E.M. / Huang, O.W. / Poy, F. / Oppikofer, M. / Bellon, S.F. / Tang, Y. / Cochran, A.G.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Mar 9, 2016Group: Experimental preparation
Revision 1.4Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5232
Polymers12,4441
Non-polymers781
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint2 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.145, 68.546, 105.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

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Components

#1: Protein Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8 / BRD9


Mass: 12444.461 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 17-123)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 2, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 21295 / % possible obs: 96.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Χ2: 1.04 / Net I/av σ(I): 29.094 / Net I/σ(I): 10.6 / Num. measured all: 123026
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.47-1.524.90.45217461.09180.8
1.52-1.585.40.39318991.09787.5
1.58-1.665.60.32421171.04297
1.66-1.745.90.25121901.008100
1.74-1.856.10.18421821.056100
1.85-26.10.12521781.004100
2-2.26.10.07622041.027100
2.2-2.516.10.06322231.004100
2.51-3.1760.05122281.0499.9
3.17-505.60.03923281.06399

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HME

3hme


Resolution: 1.47→32.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.699 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1087 5.1 %RANDOM
Rwork0.2169 ---
obs0.2178 20147 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.87 Å2 / Biso mean: 28.83 Å2 / Biso min: 15.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2--3.48 Å20 Å2
3----3.82 Å2
Refinement stepCycle: final / Resolution: 1.47→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 4 100 929
Biso mean--33.72 34.67 -
Num. residues----101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.019850
X-RAY DIFFRACTIONr_angle_refined_deg2.7641.9671141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6645100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17823.78437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95715159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.017153
X-RAY DIFFRACTIONr_chiral_restr0.20.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021631
X-RAY DIFFRACTIONr_mcbond_it2.452.192403
X-RAY DIFFRACTIONr_mcangle_it3.3273.274502
X-RAY DIFFRACTIONr_scbond_it4.1532.613447
LS refinement shellResolution: 1.471→1.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 68 -
Rwork0.235 1186 -
all-1254 -
obs--79.07 %
Refinement TLS params.Method: refined / Origin x: -8.4286 Å / Origin y: 12.125 Å / Origin z: 13.3628 Å
111213212223313233
T0.0154 Å20.001 Å20.0045 Å2-0.0118 Å2-0.0127 Å2--0.0272 Å2
L0.4164 °2-0.1818 °2-0.4439 °2-0.5895 °2-0.3988 °2--1.2835 °2
S-0.0333 Å °-0.0016 Å °-0.0258 Å °0.062 Å °-0.0159 Å °-0.0127 Å °0.0114 Å °0.0483 Å °0.0492 Å °

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