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- PDB-5l8t: Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-... -

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Basic information

Entry
Database: PDB / ID: 5l8t
TitleCrystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 2
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
Chem-6RR / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLolli, G. / Marchand, J.-R. / Caflisch, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Swiss Cancer League Switzerland
CitationJournal: J. Med. Chem. / Year: 2016
Title: Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation.
Authors: Marchand, J.R. / Lolli, G. / Caflisch, A.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 10, 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)13,7722
Polymers13,5321
Non-polymers2401
Water1,802100
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)80.827, 96.382, 57.663
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 (residues 1858-1971)
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-6RR / ~{N}-[(3~{R})-1,1-bis(oxidanylidene)thian-3-yl]-2-methyl-pyridin-3-amine


Mass: 240.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 70.36 % / Mosaicity: 0.35 °
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: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→48.19 Å / Num. obs: 19481 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.896.10.824199.8
9.06-48.195.90.024197

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ir5


Resolution: 1.85→48.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.2092 978 5.07 %
Rwork0.1877 --
obs0.1888 19288 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.33 Å2 / Biso mean: 43.2529 Å2 / Biso min: 20.19 Å2
Refinement stepCycle: final / Resolution: 1.85→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 16 100 1063
Biso mean--37.54 48.15 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061004
X-RAY DIFFRACTIONf_angle_d1.0691356
X-RAY DIFFRACTIONf_chiral_restr0.038145
X-RAY DIFFRACTIONf_plane_restr0.004171
X-RAY DIFFRACTIONf_dihedral_angle_d17.272395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.94760.33931560.29842518X-RAY DIFFRACTION98
1.9476-2.06960.30511460.24192589X-RAY DIFFRACTION99
2.0696-2.22940.22361140.21112622X-RAY DIFFRACTION99
2.2294-2.45380.2291360.19712596X-RAY DIFFRACTION99
2.4538-2.80880.24931370.19092580X-RAY DIFFRACTION97
2.8088-3.53870.21051310.19162659X-RAY DIFFRACTION99
3.5387-48.190.17271580.1632746X-RAY DIFFRACTION99
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)
15.51140.5414-1.87560.0661-0.17020.641-0.4007-0.6364-0.8768-0.0140.05930.1153-0.10210.31840.33370.37660.00550.07340.4840.10550.51681.4615-34.6835-9.9373
22.7684-0.2361-0.6111.77410.96752.68190.03180.11370.0919-0.152-0.1010.0934-0.3677-0.0620.06430.30820.0206-0.03840.2350.01250.2291-20.2162-17.7437-3.933
33.212-0.8932-0.53014.68110.29043.4873-0.378-0.5378-0.0730.77860.1603-0.19320.07950.27420.07420.3940.0601-0.06710.32140.03940.213-17.5232-19.91877.4053
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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