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- PDB-6ppa: Crystal structure of the unliganded bromodomain of human BRD7 -

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Basic information

Entry
Database: PDB / ID: 6ppa
TitleCrystal structure of the unliganded bromodomain of human BRD7
ComponentsBromodomain-containing protein 7
KeywordsGENE REGULATION / BRD7 / PBAF / CELTIX-1 / mSWI/SNF / BP75
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / regulation of mitotic cell cycle / positive regulation of cell differentiation / lysine-acetylated histone binding / kinetochore / Wnt signaling pathway / nuclear matrix / transcription corepressor activity / p53 binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / cell cycle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
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
PHOSPHATE ION / Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
Model detailsAPO
AuthorsChan, A. / Karim, M.R. / Zhu, J. / 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
DepositionJul 5, 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)14,6144
Polymers14,3951
Non-polymers2193
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bromodomain-containing protein 7
hetero molecules

A: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2288
Polymers28,7892
Non-polymers4386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area2610 Å2
ΔGint-8 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.300, 99.360, 37.830
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-466-

HOH

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Components

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


Mass: 14394.644 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 130-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD7, BP75, CELTIX1 / Plasmid: pET15-b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -RIPL / References: UniProt: Q9NPI1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7.5 MG/ML BRD7, 25MM PHOSPHATE PH 6.9, 25MM AMMONIUM SULPHATE, 0.5MM DTT, 25MM BIS-TRIS PH6.5, 15% PENTAERYTHRYTOL ETHOXYLATE 15/4EO/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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2016
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→35.65 Å / Num. obs: 13502 / % possible obs: 99.9 % / Redundancy: 7.084 % / Biso Wilson estimate: 27.232 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 0.992 / Net I/σ(I): 20.33 / Num. measured all: 95652
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
1.77-1.826.9580.3236.0968479839840.9670.35100
1.82-1.877.0040.2677.2166759539530.9810.288100
1.87-1.926.9440.2118.6664589329300.9850.22899.8
1.92-1.986.9410.16710.5663169109100.9880.18100
1.98-2.046.9550.1511.7361418848830.9920.16299.9
2.04-2.127.0890.11514.7861048638610.9940.12499.8
2.12-2.27.2390.09318.2958498088080.9950.1100
2.2-2.297.3120.08319.9157037817800.9960.0999.9
2.29-2.397.2910.07621.7356147707700.9970.082100
2.39-2.57.3430.07123.3553687317310.9970.076100
2.5-2.647.3110.0626.7550746956940.9980.06499.9
2.64-2.87.2420.05827.347946626620.9980.063100
2.8-2.997.2560.05429.9945136226220.9980.058100
2.99-3.237.1520.05132.1241985875870.9980.055100
3.23-3.547.180.04834.6138275345330.9960.05299.8
3.54-3.967.0610.04636.5134954954950.9970.049100
3.96-4.576.9790.04536.8630504374370.9960.049100
4.57-5.66.8670.04335.726373863840.9980.04799.5
5.6-7.926.640.04734.7719923003000.9980.052100
7.92-35.655.6010.05133.129971831780.9980.05697.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3hme


Resolution: 1.77→35.65 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 675 5 %
Rwork0.172 12825 -
obs0.1735 13500 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.31 Å2 / Biso mean: 27.3255 Å2 / Biso min: 11.98 Å2
Refinement stepCycle: final / Resolution: 1.77→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 13 123 1094
Biso mean--58.43 34.08 -
Num. residues----117
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.77-1.90670.24521340.21512529
1.9067-2.09850.23491320.1812521
2.0985-2.40210.18651340.16552536
2.4021-3.02620.20751350.17762561
3.0262-35.650.19091400.1622678
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)
12.7566-0.52953.02344.4385-0.42875.19960.2459-0.4165-0.46530.1926-0.2416-0.1276-0.1038-0.066-0.00920.1914-0.02320.00190.15060.02070.10992.405824.186724.3801
25.26961.196-0.03180.9821-0.29761.38660.4447-0.38870.55790.3347-0.14490.3999-0.2073-0.1157-0.17940.24090.0260.12690.15760.00420.268112.197438.66324.6842
34.62771.2187-1.57433.2265-0.88361.60160.05340.29090.3492-0.06750.18140.3402-0.0814-0.2153-0.21780.20030.02590.04670.18550.04370.145617.794938.392513.9071
44.04744.0331-3.82096.2599-2.27957.0230.389-0.3238-0.04420.266-0.138-0.0893-0.16320.2565-0.04180.12850.01880.01050.1591-0.00750.10628.119932.005622.2912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 232 through 248 )A232 - 248
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 160 )A132 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 210 )A161 - 210
4X-RAY DIFFRACTION4chain 'A' and (resid 211 through 231 )A211 - 231

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