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- PDB-6v1f: Crystal structure of the bromodomain of human BRD7 bound to BI9564 -

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Basic information

Entry
Database: PDB / ID: 6v1f
TitleCrystal structure of the bromodomain of human BRD7 bound to BI9564
ComponentsBromodomain-containing protein 7
KeywordsGENE REGULATION / BRD7 / non-BET / BRD9 / BI9564 / BP75 / CELTIX1
Function / homology
Function and homology information


histone H3K14ac reader activity / regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of double-strand break repair / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation ...histone H3K14ac reader activity / regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of double-strand break repair / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / Regulation of TP53 Activity through Acetylation / : / transcription initiation-coupled chromatin remodeling / regulation of mitotic cell cycle / positive regulation of cell differentiation / kinetochore / Wnt signaling pathway / nuclear matrix / p53 binding / transcription corepressor activity / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5U6 / Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChan, A. / Karim, M.R. / 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 20, 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9472
Polymers14,5941
Non-polymers3531
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.490, 108.710, 36.650
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-408-

HOH

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Components

#1: Protein Bromodomain-containing protein 7 / 75 kDa bromodomain protein / Protein CELTIX-1


Mass: 14593.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD7, BP75, CELTIX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q9NPI1
#2: Chemical ChemComp-5U6 / 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one


Mass: 353.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05 M (NH4)2SO4, 0.1 M Bis-tris (pH 6.5), and 30 % Pentaerythritol ethoxylate

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→32.322 Å / Num. obs: 10022 / % possible obs: 99.8 % / Redundancy: 7.12 % / Biso Wilson estimate: 30.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.046 / Χ2: 0.98 / Net I/σ(I): 28.83 / Num. measured all: 71354 / Scaling rejects: 23
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
2-2.057.2720.3086.4653817407400.9830.332100
2.05-2.117.3330.2498.0451487047020.9880.26899.7
2.11-2.177.2990.2069.7950957026980.9880.22299.4
2.17-2.247.2860.15912.647876586570.9930.17199.8
2.24-2.317.2920.14114.4147406506500.9930.152100
2.31-2.397.2680.12315.246086356340.9950.13399.8
2.39-2.487.2520.1011943516006000.9960.109100
2.48-2.587.2240.07223.9343135995970.9980.07899.7
2.58-2.77.1610.0627.2639535535520.9980.06599.8
2.7-2.837.1530.0531.7339345505500.9990.055100
2.83-2.987.0590.04734.6136925235230.9990.051100
2.98-3.167.1170.04239.9733954784770.9990.04599.8
3.16-3.387.0890.03547.8533394724710.9990.03899.8
3.38-3.656.9750.02954.7630694404400.9990.032100
3.65-47.010.02758.01275539339310.029100
4-4.476.8880.02460.0425283673670.9990.026100
4.47-5.166.7960.02459.52222932932810.02699.7
5.16-6.326.6740.02559.6618622792790.9990.027100
6.32-8.946.3950.02961.1514582302280.9990.03199.1
8.94-32.3225.2720.02854.97171401360.9990.03297.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PPA

6ppa


Resolution: 2→32.322 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 500 4.99 %
Rwork0.217 9516 -
obs0.2187 10016 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.93 Å2 / Biso mean: 37.865 Å2 / Biso min: 20.22 Å2
Refinement stepCycle: final / Resolution: 2→32.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 26 29 1013
Biso mean--43.63 37.32 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031005
X-RAY DIFFRACTIONf_angle_d0.5781349
X-RAY DIFFRACTIONf_chiral_restr0.038141
X-RAY DIFFRACTIONf_plane_restr0.006169
X-RAY DIFFRACTIONf_dihedral_angle_d4.088621
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0001-2.20130.23321220.22272335
2.2013-2.51970.26691230.22912337
2.5197-3.17420.25671250.2492360
3.1742-32.3220.24351300.1992484
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)
13.94952.7711-2.35582.7281-0.42743.35320.2646-0.5679-0.65070.09440.0779-0.48770.51990.0237-0.13430.32180.0354-0.12880.56380.05710.198728.712615.840143.219
21.94020.9469-0.19614.81762.23971.26340.3222-0.534-0.93790.00480.2630.04620.578-0.2999-0.28020.3595-0.0165-0.17320.34020.20570.488411.03396.981137.6758
34.61581.4794-1.30743.39631.85752.14650.2750.5881-1.0389-1.34790.43060.44070.494-0.3845-0.42760.51070.0888-0.36340.3026-0.09180.47786.55148.362725.3085
47.15570.89623.20562.41910.73412.4577-0.02650.1506-0.6748-0.09650.251-0.19540.16220.3745-0.21180.27130.0352-0.02510.3103-0.02770.156620.596715.68732.5543
55.41290.76750.99974.87840.17293.51250.0469-0.96680.0880.34970.20920.50910.0628-0.3562-0.31890.25680.05490.02480.51850.050.19437.747420.209839.9431
62.90220.5053-2.98043.55930.20593.63240.0608-0.21310.43660.0599-0.09210.1504-0.3577-0.08390.14320.3415-0.0416-0.04070.42210.01130.200433.07627.977741.3451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 150 )A132 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 165 )A151 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 171 )A166 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 210 )A172 - 210
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 231 )A211 - 231
6X-RAY DIFFRACTION6chain 'A' and (resid 232 through 248 )A232 - 248

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