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- PDB-5orb: Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-c... -

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Basic information

Entry
Database: PDB / ID: 5orb
TitleCrystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 30
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-JR6 / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å
AuthorsLolli, G. / Dalle Vedove, A. / Marchand, J.-R. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss Cancer Society (Krebsliga Schweiz)KLS-3098- 02-2013 Switzerland
CitationJournal: J Chem Inf Model / Year: 2017
Title: Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking.
Authors: Marchand, J.R. / Dalle Vedove, A. / Lolli, G. / Caflisch, A.
History
DepositionAug 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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)13,9983
Polymers13,6191
Non-polymers3792
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint3 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.906, 96.788, 57.820
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: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1858-1972
Mutation: First two residues SM derive from the expression tag
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-JR6 / 2-(4-methoxyphenyl)sulfanyl-~{N}-(2-methyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)ethanamide


Mass: 317.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O2S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.103→48.394 Å / Num. obs: 9775 / % possible obs: 72.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) all% possible all
6.634-48.39470.0626.10.9960.026100
2.103-2.1697.20.5423.90.9370.2141.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DYU

5dyu


Resolution: 2.103→48.394 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81
Details: Data were strongly anisotropic. Data were subjected to ellipsoidal processing through the Staraniso server (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). As such, spherical ...Details: Data were strongly anisotropic. Data were subjected to ellipsoidal processing through the Staraniso server (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). As such, spherical completeness is low overall and in highest resolution shells. Included data contribute however relevantly to the density maps.
RfactorNum. reflection% reflection
Rfree0.2182 514 5.27 %
Rwork0.1876 --
obs0.1893 9759 72.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.53 Å2 / Biso mean: 31.9924 Å2 / Biso min: 8.43 Å2
Refinement stepCycle: final / Resolution: 2.103→48.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 26 99 1072
Biso mean--58.82 40 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061015
X-RAY DIFFRACTIONf_angle_d0.7581367
X-RAY DIFFRACTIONf_chiral_restr0.043144
X-RAY DIFFRACTIONf_plane_restr0.004172
X-RAY DIFFRACTIONf_dihedral_angle_d16.492629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1032-2.31480.2373830.18221432151545
2.3148-2.64980.249950.20031806190157
2.6498-3.33830.2691420.20062706284884
3.3383-48.40680.19271940.179833013495100
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)
10.02090.02170.01270.02720.03630.0143-0.04270.0182-0.1123-0.11430.04370.2071-0.08740.11230.01510.1104-0.08960.03650.37160.08040.26681.283-34.7727-9.865
20.0145-0.00190.0169-0.002-0.00380.0218-0.01240.0279-0.0316-0.0333-0.07460.05450.1003-0.0834-0.04640.0832-0.0228-0.0470.0963-0.01740.2019-20.4635-29.8752-2.0899
30.1986-0.0077-0.08320.0677-0.03470.34860.16060.05140.015-0.0507-0.1023-0.0526-0.38920.11070.03940.1665-0.0057-0.0080.1238-0.00830.1116-20.3863-14.9387-4.4675
40.01830.010.0210.0065-0.00330.0853-0.0013-0.1566-0.00810.1813-0.0504-0.0216-0.09670.2065-0.0330.22540.1041-0.04960.07910.04370.0979-17.6618-19.85917.4849
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 1943 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1944 through 1971 )A0

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