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- PDB-5mgg: Crystal Structure of BAZ2B bromodomain in complex with 4-chloropy... -

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Basic information

Entry
Database: PDB / ID: 5mgg
TitleCrystal Structure of BAZ2B bromodomain in complex with 4-chloropyridine derivative 3
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-chloranyl-~{N}-methyl-pyridine-2-carboxamide / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 / Refinement description / Category: citation / citation_author / 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 / 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 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7022
Polymers13,5321
Non-polymers1711
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.702, 96.706, 57.547
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-7MU / 4-chloranyl-~{N}-methyl-pyridine-2-carboxamide


Mass: 170.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7ClN2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 70.35 % / Mosaicity: 0.29 °
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: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.17 Å / Num. obs: 13460 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.167.10.8610.8581100
8.91-42.176.20.0260.999198.6

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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: 2.1→37.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2194 671 5.03 %
Rwork0.1834 --
obs0.1852 13341 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.42 Å2 / Biso mean: 51.5932 Å2 / Biso min: 27.68 Å2
Refinement stepCycle: final / Resolution: 2.1→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 11 65 1023
Biso mean--59.57 51.8 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008979
X-RAY DIFFRACTIONf_angle_d1.0161316
X-RAY DIFFRACTIONf_chiral_restr0.037141
X-RAY DIFFRACTIONf_plane_restr0.004167
X-RAY DIFFRACTIONf_dihedral_angle_d14.564374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.26230.34061280.28312485261399
2.2623-2.48990.27131540.21662472262699
2.4899-2.85010.25791300.18712503263398
2.8501-3.59030.23461280.19392543267199
3.5903-37.02560.17881310.15842667279899
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)
14.74971.09160.95120.37110.26390.2131-0.4892-0.66940.2482-0.09990.0885-0.3106-0.0546-0.3270.38090.46390.0103-0.08560.5731-0.06610.6044-1.314234.6618-9.8619
28.8793-4.84694.34944.4099-3.04384.0839-0.19170.03770.95620.1683-0.0705-0.5187-0.47660.20630.18170.3296-0.04110.04010.3627-0.01670.461820.546629.5633-2.0809
32.16321.19980.49423.96140.46761.84330.0952-0.1262-0.4508-0.3014-0.0113-0.36370.5334-0.067-0.04280.50410.02030.00130.34280.00910.378324.89310.1268-2.9457
42.3232-0.67841.03963.8321-2.14943.7949-0.01330.2251-0.0082-0.41550.15730.17420.5435-0.2976-0.11810.3821-0.06140.02310.3778-0.00790.318316.666619.2464-5.3455
53.4979-1.49450.48266.0135-0.20773.3961-0.3904-0.60040.16830.67720.49870.07270.0173-0.3221-0.18460.51280.01660.05720.4465-0.03950.314317.57420.17377.4602
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 1882 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1883 through 1910 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1911 through 1943 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1944 through 1971 )A0

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