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- PDB-5mgm: Crystal Structure of BAZ2A bromodomain in complex with acetopheno... -

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Basic information

Entry
Database: PDB / ID: 5mgm
TitleCrystal Structure of BAZ2A bromodomain in complex with acetophenone derivative 4
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / 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
1-(3-pyrimidin-2-yloxyphenyl)ethanone / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLolli, G. / Spiliotopoulos, D. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_169007 Switzerland
CitationJournal: Eur J Med Chem / Year: 2017
Title: Discovery of BAZ2A bromodomain ligands.
Authors: Spiliotopoulos, D. / Wamhoff, E.C. / Lolli, G. / Rademacher, C. / Caflisch, A.
History
DepositionNov 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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 / diffrn_radiation_wavelength / 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 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5952
Polymers12,3811
Non-polymers2141
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.861, 94.861, 32.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / hWALp3


Mass: 12380.919 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1796-1898
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-7MZ / 1-(3-pyrimidin-2-yloxyphenyl)ethanone


Mass: 214.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.44 Å3/Da / Density % sol: 64.2 % / Mosaicity: 1 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2

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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: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→27.38 Å / Num. obs: 4298 / % possible obs: 99.5 % / Redundancy: 9.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.318 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.8-2.958.71.3470.6991100
8.86-27.3810.30.0990.997197

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LZ2

4lz2


Resolution: 2.8→27.38 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 10.97 / SU ML: 0.211 / SU R Cruickshank DPI: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 187 4.4 %RANDOM
Rwork0.2181 ---
obs0.2195 4109 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.01 Å2 / Biso mean: 41.931 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-13.16 Å20 Å20 Å2
2--13.16 Å20 Å2
3----26.32 Å2
Refinement stepCycle: final / Resolution: 2.8→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 16 23 868
Biso mean--31.28 23.55 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.019867
X-RAY DIFFRACTIONr_bond_other_d0.0010.02781
X-RAY DIFFRACTIONr_angle_refined_deg0.8731.9611167
X-RAY DIFFRACTIONr_angle_other_deg0.67631791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23922.91748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96815145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.716159
X-RAY DIFFRACTIONr_chiral_restr0.0470.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
X-RAY DIFFRACTIONr_mcbond_it1.1474.189399
X-RAY DIFFRACTIONr_mcbond_other1.134.179398
X-RAY DIFFRACTIONr_mcangle_it2.0946.265497
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 7 -
Rwork0.342 316 -
all-323 -
obs--99.69 %

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