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- PDB-5e73: Crystal Structure of BAZ2B bromodomain in complex with acetylindo... -

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Basic information

Entry
Database: PDB / ID: 5.0E+73
TitleCrystal Structure of BAZ2B bromodomain in complex with acetylindole compound UZH47
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-UO1 / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsLolli, G. / Spiliotopoulos, D. / Unzue, A. / Nevado, C. / Caflisch, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss Cancer Society (Krebsliga) Switzerland
Swiss National Science Foundation Switzerland
CitationJournal: J. Med. Chem. / Year: 2016
Title: The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains.
Authors: Unzue, A. / Zhao, H. / Lolli, G. / Dong, J. / Zhu, J. / Zechner, M. / Dolbois, A. / Caflisch, A. / Nevado, C.
History
DepositionOct 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: 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)13,8542
Polymers13,5321
Non-polymers3221
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.175, 96.477, 57.727
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 1858-1971
Mutation: First two residues SM derive from the expression tag
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-UO1 / N-(1-acetyl-1H-indol-3-yl)-N-(5-hydroxy-2-methylphenyl)acetamide


Mass: 322.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 4.28 Å3/Da / Density % sol: 71.26 %
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: 0.915 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.71→42.56 Å / Num. obs: 25278 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.026 / Net I/σ(I): 15.6 / Num. measured all: 110426
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.71-1.744.40.8581.9582713230.7740.467100
9.05-42.564.20.018468662070.9990.00998.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR5

4ir5


Resolution: 1.71→33.743 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1241 4.98 %
Rwork0.1904 23701 -
obs0.1915 24942 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.09 Å2 / Biso mean: 33.5187 Å2 / Biso min: 14.83 Å2
Refinement stepCycle: final / Resolution: 1.71→33.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 24 189 1160
Biso mean--31.95 42.73 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071008
X-RAY DIFFRACTIONf_angle_d1.0961364
X-RAY DIFFRACTIONf_chiral_restr0.043144
X-RAY DIFFRACTIONf_plane_restr0.004172
X-RAY DIFFRACTIONf_dihedral_angle_d14.756391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.77850.31611340.28232613274798
1.7785-1.85940.33151220.26282652277499
1.8594-1.95740.37231210.3372458257993
1.9574-2.08010.26941490.25452566271597
2.0801-2.24060.25141520.21932628278099
2.2406-2.46610.24521230.20942634275797
2.4661-2.82280.22341270.18312670279799
2.8228-3.55580.20841530.17652700285399
3.5558-33.74960.14871600.14542780294099
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)
19.50311.3946-5.42280.225-0.79073.0566-0.5162-0.8162-0.7963-0.2929-0.01870.0474-0.06390.4980.58330.30430.0065-0.01690.41110.06930.40031.9648-33.9913-9.7884
29.7832-5.1736-4.6024.89123.23424.4056-0.29490.1196-0.72850.25350.05790.37480.43050.05640.19350.25610.0046-0.00290.1838-00.3034-20.6074-29.5257-2.3065
33.7421-0.0011-0.90366.761-0.08982.73050.0374-0.02320.4616-0.31080.08230.1799-0.2646-0.032-0.11170.17740.0285-0.00910.1357-0.00470.1737-25.8677-10.2247-3.0382
43.883-2.2314-0.51064.05640.15932.5040.16480.19180.0784-0.1595-0.0924-0.19490.05490.1505-0.05370.14770.0075-0.00510.14550.00990.1283-17.4013-19.067-5.4756
51.82840.69051.59787.47822.05665.3047-0.228-1.09160.46221.41260.55540.1213-0.942-0.010.05290.5010.1024-0.01980.4897-0.10410.2965-23.6913-6.86811.2223
63.9808-1.3960.01285.7426-0.11964.7303-0.51-0.528-0.1720.93040.3633-0.13440.62320.49410.04670.3150.0754-0.01710.25510.02710.1514-16.9754-22.85876.467
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 1948 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1949 through 1971 )A0

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