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- PDB-6uzf: Crystal structure of the unliganded bromodomain of human BRD9 -

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Basic information

Entry
Database: PDB / ID: 6uzf
TitleCrystal structure of the unliganded bromodomain of human BRD9
ComponentsBromodomain-containing protein 9
KeywordsGENE REGULATION / BRD9 / BAF / PBAF / mSWI/SNF
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 / regulation of transcription by RNA polymerase II / chromatin ...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 / regulation of transcription by RNA polymerase II / chromatin / 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 ...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: 1.75 Å
Model detailsAPO
AuthorsKarim, M.R. / Chan, A. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.
Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5485
Polymers14,2501
Non-polymers2984
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.270, 55.510, 58.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14249.763 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pNIC28 / Details (production host): pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.05 M (NH4)2SO4, 0.05 M Bis-Tris (pH 6.5), 30% Pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 30, 2017
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40.238 Å / Num. obs: 11749 / % possible obs: 99.9 % / Redundancy: 7.093 % / Biso Wilson estimate: 24.067 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Χ2: 0.974 / Net I/σ(I): 23.96 / Num. measured all: 83340 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.87.1710.5983.2762398708700.880.644100
1.8-1.847.2330.4364.5958018048020.9120.46999.8
1.84-1.97.1890.3515.5458458138130.9470.378100
1.9-1.967.210.2876.8656317827810.9680.30999.9
1.96-2.027.1280.2149.0854677707670.9830.2399.6
2.02-2.097.2230.1471353167367360.9930.159100
2.09-2.177.170.12215.7951557207190.9920.13199.9
2.17-2.267.1460.10218.0249456926920.9950.109100
2.26-2.367.2250.09220.2547116526520.9950.099100
2.36-2.487.1570.07723.445096306300.9970.083100
2.48-2.617.1410.0725.9843926156150.9980.075100
2.61-2.777.1420.05830.4840855725720.9980.062100
2.77-2.967.0220.04836.2238135455430.9990.05299.6
2.96-3.27.0620.03944.1535595045040.9990.042100
3.2-3.56.9460.03351.7833344804800.9980.035100
3.5-3.916.8760.02659.94295042942910.029100
3.91-4.526.8620.02163.91264238538510.023100
4.52-5.536.8550.02262.8222763323320.9990.024100
5.53-7.836.5380.02356.0917132622620.9990.025100
7.83-40.2385.80.01865.3795716516510.02100

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Processing

Software
NameVersionClassification
PHENIX1.14-3260_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.75→40.238 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.02
RfactorNum. reflection% reflection
Rfree0.2193 588 5.01 %
Rwork0.1778 --
obs0.1799 11748 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.79 Å2 / Biso mean: 18.8779 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.75→40.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 17 151 1016
Biso mean--36.87 29.06 -
Num. residues----104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7501-1.92620.24671440.2052733
1.9262-2.20490.24231440.18012742
2.2049-2.77790.21861460.17832776
2.7779-40.230.20341540.17092909
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5744-1.747-1.85323.98334.52545.535-0.0048-0.0035-0.0797-0.1985-0.21820.1782-0.2512-0.21970.24950.12110.0262-0.02340.13040.00070.1263-21.86848.07920.8573
24.5622-3.01011.22253.7777-1.70650.67780.0656-0.086-0.2963-0.09490.07830.17450.0765-0.045-0.12070.113-0.0084-0.0120.1294-0.00770.117-11.1276-10.89820.3738
31.2284-1.4999-1.24724.4481.89982.2286-0.139-0.22680.11090.2020.1196-0.01490.15040.03340.01710.12280.0126-0.02310.15330.02280.0823-12.9321-0.53566.128
42.4571-1.8232-0.27012.9117-0.30530.68910.0109-0.1090.18080.02460.0338-0.2047-0.1266-0.0079-0.05680.0649-0.0137-0.01530.11880.00910.0873-9.55393.76662.0092
55.29791.0139-2.89215.1273.08234.52040.07870.5627-0.7839-0.65320.2285-0.62220.85240.59750.04880.25410.0890.04360.2093-0.02280.1399-4.487-11.6713-10.8842
62.9281-2.0982-1.17442.31771.93022.91140.1590.29960.1976-0.3866-0.2076-0.0806-0.1962-0.1590.06430.14410.0127-0.00650.15920.01710.1061-12.01243.0739-9.857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 137 through 155 )A137 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 176 )A156 - 176
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 191 )A177 - 191
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 215 )A192 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 220 )A216 - 220
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 240 )A221 - 240

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