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- PDB-5ji8: Crystal structure of the BRD9 bromodomain and hit 1 -

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Basic information

Entry
Database: PDB / ID: 5ji8
TitleCrystal structure of the BRD9 bromodomain and hit 1
ComponentsBromodomain-containing protein 9
KeywordsPROTEIN BINDING / BRD9 / bromodomain
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
2-amino-1,3-benzothiazole-6-carboxamide / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWang, N. / Li, F. / Bao, H. / Li, J. / Wu, J. / Ruan, K.
CitationJournal: Chembiochem / Year: 2016
Title: NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains
Authors: Wang, N. / Li, F. / Bao, H. / Li, J. / Wu, J. / Ruan, K.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 8, 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)13,2502
Polymers13,0571
Non-polymers1931
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5970 Å2
Unit cell
Length a, b, c (Å)24.498, 34.090, 39.519
Angle α, β, γ (deg.)70.090, 75.280, 73.240
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 13057.188 Da / Num. of mol.: 1 / Fragment: UNP residues 137-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9H8M2
#2: Chemical ChemComp-6KT / 2-amino-1,3-benzothiazole-6-carboxamide


Mass: 193.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.1M Bis-Tris PH6.4, 27% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 20295 / % possible obs: 94.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 13.22 Å2 / Rmerge(I) obs: 0.05 / Net I/av σ(I): 15.305 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.42-1.442.40.202193
1.44-1.472.40.172192.6
1.47-1.52.30.149193.7
1.5-1.532.40.138192.5
1.53-1.562.30.127192.8
1.56-1.62.20.114193.7
1.6-1.642.30.108194.6
1.64-1.682.40.101194.8
1.68-1.732.40.092194.6
1.73-1.792.30.079195.3
1.79-1.852.20.076194.2
1.85-1.932.20.074195.2
1.93-2.012.40.069195.7
2.01-2.122.40.062195.4
2.12-2.252.40.062196.2
2.25-2.432.20.055196.3
2.43-2.672.40.052196.9
2.67-3.062.40.048197.5
3.06-3.852.20.044197.1
3.85-502.40.04196.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.42→28.107 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 19.25
RfactorNum. reflection% reflection
Rfree0.1704 918 4.98 %
Rwork0.1497 --
obs0.1507 18442 86.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52 Å2 / Biso mean: 22.0771 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: final / Resolution: 1.42→28.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 20 156 979
Biso mean--31.84 29.41 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009851
X-RAY DIFFRACTIONf_angle_d0.9071149
X-RAY DIFFRACTIONf_chiral_restr0.066121
X-RAY DIFFRACTIONf_plane_restr0.007144
X-RAY DIFFRACTIONf_dihedral_angle_d18.624318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4205-1.49540.2166700.1871590166055
1.4954-1.58910.1899970.15862151224874
1.5891-1.71170.18291510.14862647279891
1.7117-1.8840.16651570.152774293195
1.884-2.15650.16741280.14342746287495
2.1565-2.71660.18041380.15032841297997
2.7166-28.11250.16231770.14812775295297
Refinement TLS params.Method: refined / Origin x: 0.8912 Å / Origin y: 0.7266 Å / Origin z: 1.3584 Å
111213212223313233
T0.0752 Å20.0092 Å2-0.0054 Å2-0.0872 Å20.0282 Å2--0.0686 Å2
L4.0718 °20.2847 °2-0.5373 °2-2.8556 °20.349 °2--2.2993 °2
S-0.0688 Å °-0.1772 Å °0.0807 Å °0.0031 Å °0.0438 Å °0.0326 Å °0.0778 Å °0.0149 Å °0.0232 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA139 - 238
2X-RAY DIFFRACTION1allC1 - 169
3X-RAY DIFFRACTION1allB0

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