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- PDB-6fgt: Crystal Structure of BAZ2B bromodomain in complex with 1-methylpy... -

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Basic information

Entry
Database: PDB / ID: 6fgt
TitleCrystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 3
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / DNA binding / zinc ion binding / nucleus
Similarity search - Function
BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain ...BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-D9T / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDalle Vedove, A. / Spiliotopoulos, D. / Lolli, G. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_169007 Switzerland
CitationJournal: ChemMedChem / Year: 2018
Title: Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains.
Authors: Dalle Vedove, A. / Spiliotopoulos, D. / D'Agostino, V.G. / Marchand, J.R. / Unzue, A. / Nevado, C. / Lolli, G. / Caflisch, A.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / 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 1.2Jan 17, 2024Group: 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 adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8822
Polymers13,6191
Non-polymers2631
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.607, 95.970, 57.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 13618.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8
#2: Chemical ChemComp-D9T / ~{N}-[(1-azanylcyclohexyl)methyl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide


Mass: 263.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.15 Å3/Da / Density % sol: 70.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.29 Å / Num. obs: 15653 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1148 / CC1/2: 0.983 / Rpim(I) all: 0.162 / Rrim(I) all: 0.451 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DYU

5dyu


Resolution: 2→40.803 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.32
RfactorNum. reflection% reflection
Rfree0.2388 736 4.75 %
Rwork0.2142 --
obs0.2154 15492 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 19 71 1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061015
X-RAY DIFFRACTIONf_angle_d0.8691369
X-RAY DIFFRACTIONf_dihedral_angle_d18.472616
X-RAY DIFFRACTIONf_chiral_restr0.041144
X-RAY DIFFRACTIONf_plane_restr0.004171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.15440.34771530.28482908X-RAY DIFFRACTION99
2.1544-2.37120.31611420.25222873X-RAY DIFFRACTION98
2.3712-2.71430.24831500.21452936X-RAY DIFFRACTION99
2.7143-3.41940.26781310.22672975X-RAY DIFFRACTION99
3.4194-40.8120.19691600.18973064X-RAY DIFFRACTION99

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