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- PDB-5mge: Crystal structure of BAZ2B bromodomain in complex with 1-methylpy... -

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Basic information

Entry
Database: PDB / ID: 5mge
TitleCrystal structure of BAZ2B bromodomain in complex with 1-methylpyridine derivative 1
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-7MX / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / software
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 / 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)13,7472
Polymers13,5321
Non-polymers2161
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.949, 96.753, 57.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 13531.574 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 2054-2167
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: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8
#2: Chemical ChemComp-7MX / ethyl 4-chloranyl-1-methyl-6-oxidanylidene-pyridine-3-carboxylate


Mass: 215.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10ClNO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 4.14 Å3/Da / Density % sol: 70.31 % / Mosaicity: 0.26 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG500MME (20%), PEG1000 (2%), PEG3350 (2%), PEG20000 (10%), MPD (2%)

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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 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.38 Å / Num. obs: 16759 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-27.70.785895311650.930.3020.8422.299.7
8.94-48.386.60.03113632080.9990.0120.03439.799.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR5

4ir5


Resolution: 1.95→48.376 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2183 849 5.09 %
Rwork0.1804 --
obs0.1823 16672 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.23 Å2 / Biso mean: 42.1416 Å2 / Biso min: 19.52 Å2
Refinement stepCycle: final / Resolution: 1.95→48.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 14 104 1065
Biso mean--44.66 47.72 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006982
X-RAY DIFFRACTIONf_angle_d0.9961321
X-RAY DIFFRACTIONf_chiral_restr0.034141
X-RAY DIFFRACTIONf_plane_restr0.003167
X-RAY DIFFRACTIONf_dihedral_angle_d13.886375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.07220.25641600.24592556271699
2.0722-2.23220.25861430.21782595273899
2.2322-2.45690.25391230.20452611273499
2.4569-2.81230.22871280.20182642277099
2.8123-3.54310.24811450.1926562801100
3.5431-48.39140.1751500.148627632913100
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)
10.0060.0173-0.00090.0688-0.0020.0696-0.4597-0.4313-0.2437-0.2299-0.07750.1473-0.48870.2707-0.02070.2957-0.00940.01830.53490.03930.47381.4776-35.107-9.8861
21.2147-0.78540.48730.5528-0.1370.83820.0560.0115-0.0627-0.0157-0.0173-0.0122-0.32080.074800.2430.00470.00360.2418-0.00630.252-20.0081-17.6433-3.915
30.18010.04360.00160.0351-0.09150.3296-0.2464-0.2566-0.18040.640.0760.1739-0.10210.1207-0.00040.40530.0804-0.02120.33840.03680.2658-17.0689-20.16667.3598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1856 through 1868 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1869 through 1943 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1944 through 1971 )A0

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