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- PDB-7tab: G-925 bound to the SMARCA4 (BRG1) Bromodomain -

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Basic information

Entry
Database: PDB / ID: 7tab
TitleG-925 bound to the SMARCA4 (BRG1) Bromodomain
ComponentsIsoform 4 of Transcription activator BRG1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bromodomain BRG1 SMARCA4 inhibitor / protein binding / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyHydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 2-(6-amino-5-phenylpyridazin-3-yl)phenol / Isoform 4 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsTang, Y. / Poy, F. / Taylor, A.M. / Cochran, A.G. / Bellon, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1.
Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, ...Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, S. / Leblanc, Y. / Murray, J. / Nasveschuk, C.G. / Neiss, A. / Poy, F. / Romero, F.A. / Sandy, P. / Tang, Y. / Tsui, V. / Zawadzke, L. / Sims 3rd, R.J. / Audia, J.E. / Bellon, S.F. / Magnuson, S.R. / Albrecht, B.K. / Cochran, A.G.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 4 of Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,1041
Non-polymers2631
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.227, 28.597, 65.740
Angle α, β, γ (deg.)90.000, 91.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoform 4 of Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 15104.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532-4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GGU / 2-(6-amino-5-phenylpyridazin-3-yl)phenol


Mass: 263.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.74 %
Description: Very thin plates that nonetheless diffract to extreme high resolution.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein in buffer: 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, at a concentration of 15.55 mg/ml (1.03 mM) Reservoir solution contains: Jeffamine ED-2001 pH 7.0 at 30%, Tris-HCl pH 8.5 at 0.1 M, 4% PEG 400
PH range: 8.2-8.8 / Temp details: 4 degree Celsius

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98011 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 38722 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Χ2: 1.036 / Net I/σ(I): 8.6 / Num. measured all: 134810
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.16-1.22.80.5733491.054186.4
1.2-1.253.40.50338981.0611100
1.25-1.313.50.37139431.0111100
1.31-1.383.60.28139161.0231100
1.38-1.463.60.20938831.0671100
1.46-1.573.60.14539161.0281100
1.57-1.733.60.11239211.002199.9
1.73-1.983.60.08939501.044199.7
1.98-2.53.60.06439321.028199.5
2.5-503.40.0540141.051198.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GRC

2grc


Resolution: 1.16→32.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.434 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1943 5 %RANDOM
Rwork0.1798 ---
obs0.1809 36670 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.28 Å2 / Biso mean: 13.091 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å2-0.03 Å2
2--0.19 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.16→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 20 126 1158
Biso mean--10.6 19 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121063
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.6441429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97915219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.363157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02785
LS refinement shellResolution: 1.16→1.189 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.163 114 -
Rwork0.167 2252 -
obs--81.59 %

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