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- PDB-5l8u: Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-... -

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Basic information

Entry
Database: PDB / ID: 5l8u
TitleCrystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 5
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-6RS / TRIETHYLENE GLYCOL / 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)14,1164
Polymers13,5321
Non-polymers5853
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint6 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.312, 96.813, 57.716
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 1954-2067)
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-6RS / ~{N}-[(1~{S})-1-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)ethyl]-2-methyl-pyridin-3-amine


Mass: 284.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 4.2 Å3/Da / Density % sol: 70.69 % / 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: 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→48.41 Å / Num. obs: 19825 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 17.1 / Num. measured all: 124446
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.8960.874199.9
9.06-48.415.70.034199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ir5


Resolution: 1.85→48.407 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.99
RfactorNum. reflection% reflection
Rfree0.1922 994 5.04 %
Rwork0.1736 --
obs0.1745 19717 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.65 Å2 / Biso mean: 40.93 Å2 / Biso min: 20.24 Å2
Refinement stepCycle: final / Resolution: 1.85→48.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 35 130 1112
Biso mean--60.82 48.5 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071016
X-RAY DIFFRACTIONf_angle_d1.0161364
X-RAY DIFFRACTIONf_chiral_restr0.036144
X-RAY DIFFRACTIONf_plane_restr0.004171
X-RAY DIFFRACTIONf_dihedral_angle_d16.112394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.94750.27911530.24332587274098
1.9475-2.06960.26491510.20226272778100
2.0696-2.22940.18691170.184926672784100
2.2294-2.45370.21031360.17472659279599
2.4537-2.80870.20511430.17542655279899
2.8087-3.53850.18531330.178927262859100
3.5385-48.42310.17131610.156628022963100
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)
18.01830.4282-3.23370.0457-0.17381.231-0.45-0.7558-0.5402-0.1567-0.00250.2821-0.04560.27030.45470.4060.00160.04690.46970.02950.48621.3823-34.4224-9.7213
24.939-4.4119-6.13614.92954.77618.1674-0.42640.1183-0.61060.28510.06930.4830.7402-0.23050.34560.3041-0.0178-0.01630.22760.0210.3769-20.4814-29.6632-1.8556
32.6560.41-0.77456.3292-1.13012.65310.0713-0.03340.3035-0.3210.00240.224-0.2696-0.0998-0.07440.33480.0431-0.02740.2586-0.01740.2869-25.1326-10.208-2.9501
43.2557-1.1471-0.17724.14011.10293.05020.02560.01160.07930.02280.0424-0.1094-0.13130.1909-0.05960.2525-0.0139-0.01090.22050.01860.2073-17.7544-17.1361-2.5714
55.1013-2.8586-1.05577.81531.49164.6774-0.566-0.5372-0.28790.95290.3996-0.13390.45780.52590.10870.35970.0577-0.03410.33020.05540.2504-16.4977-22.92316.8579
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 1948 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1949 through 1971 )A0

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