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- PDB-5or9: Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-c... -

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Basic information

Entry
Database: PDB / ID: 5or9
TitleCrystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 13
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-JR5 / 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 Å
AuthorsLolli, G. / Vedove, A.D. / 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)14,0733
Polymers13,6191
Non-polymers4552
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint2 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.444, 96.646, 57.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 1954-2068
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-JR5 / (2~{S})-1-(4-fluorophenyl)sulfonyl-~{N}-(2-methyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)pyrrolidine-2-carboxamide


Mass: 392.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21FN4O3S
#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.: 93 / 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: 4.19 Å3/Da / Density % sol: 70.62 % / Mosaicity: 0.27 °
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.32 Å / Num. obs: 15678 / % possible obs: 99.7 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.057.50.66811490.9530.2580.71799.3
8.94-48.326.70.0362080.9990.0140.03998.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DYU

5dyu


Resolution: 2→40.722 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 808 5.18 %
Rwork0.1874 --
obs0.1885 15606 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 31 93 1071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061014
X-RAY DIFFRACTIONf_angle_d0.81369
X-RAY DIFFRACTIONf_dihedral_angle_d16.123622
X-RAY DIFFRACTIONf_chiral_restr0.044144
X-RAY DIFFRACTIONf_plane_restr0.004171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.12540.29091260.2732425X-RAY DIFFRACTION98
2.1254-2.28940.25671290.23112394X-RAY DIFFRACTION98
2.2894-2.51980.2221390.2022456X-RAY DIFFRACTION99
2.5198-2.88430.18991340.17822450X-RAY DIFFRACTION100
2.8843-3.63360.22261490.18852461X-RAY DIFFRACTION100
3.6336-40.73040.18041310.16652612X-RAY DIFFRACTION100
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)
10.03540.03180.0883-0.0022-0.0943-0.0348-0.2543-0.33330.2519-0.14890.0264-0.1470.2949-0.17-0.00050.33430.0164-0.04330.5552-0.03310.5146-1.464134.3934-9.7388
20.0351-0.0315-0.03510.0053-0.0287-0.006-0.10230.09130.10520.0572-0.0379-0.1378-0.26140.14100.2643-0.00160.01160.3375-0.01870.389320.435529.9085-2.0626
30.7758-0.2474-0.20530.25350.05760.68150.07260.0699-0.0899-0.1693-0.08140.01950.3812-0.01850.00010.3015-0.0080.00220.26440.00150.285320.345615.1946-4.3357
40.10140.0181-0.15420.07790.06370.5124-0.2152-0.34920.05210.51190.19840.005-0.0723-0.20580.00010.49640.06750.03020.391-0.0240.337417.610720.26467.2938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1856 through 1868 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1869 through 1882 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1883 through 1943 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1944 through 1971 )

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