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- PDB-5e9y: Crystal Structure of BAZ2B bromodomain in complex with MPD -

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Basic information

Entry
Database: PDB / ID: 5e9y
TitleCrystal Structure of BAZ2B bromodomain in complex with MPD
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
Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLolli, G. / Caflisch, A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography.
Authors: Lolli, G. / Caflisch, A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 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)13,6502
Polymers13,5321
Non-polymers1181
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-12 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.317, 96.190, 57.749
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
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 4.17 Å3/Da / Density % sol: 70.52 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.1 Å / Num. obs: 27621 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Net I/σ(I): 20.2 / Num. measured all: 181473
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
1.65-1.686.70.6332.9891513360.9380.26399.9
9.04-48.15.80.0447.911551990.9970.01898.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ir5


Resolution: 1.65→42.289 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 1400 5.08 %
Rwork0.178 26157 -
obs0.1794 27557 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.59 Å2 / Biso mean: 39.9377 Å2 / Biso min: 21.34 Å2
Refinement stepCycle: final / Resolution: 1.65→42.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 8 145 1100
Biso mean--49.34 47.48 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006975
X-RAY DIFFRACTIONf_angle_d1.0161312
X-RAY DIFFRACTIONf_chiral_restr0.035142
X-RAY DIFFRACTIONf_plane_restr0.005165
X-RAY DIFFRACTIONf_dihedral_angle_d14.282375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.7090.28811460.27992581X-RAY DIFFRACTION100
1.709-1.77740.31131330.24072557X-RAY DIFFRACTION100
1.7774-1.85830.23241210.21552621X-RAY DIFFRACTION100
1.8583-1.95630.20071330.20432579X-RAY DIFFRACTION100
1.9563-2.07880.2211500.19782585X-RAY DIFFRACTION100
2.0788-2.23930.20571380.17722606X-RAY DIFFRACTION100
2.2393-2.46470.21141480.1762599X-RAY DIFFRACTION100
2.4647-2.82130.24041420.17652623X-RAY DIFFRACTION100
2.8213-3.55420.21451430.18672653X-RAY DIFFRACTION100
3.5542-42.2890.17041460.15662753X-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)
13.2044-0.523-0.66630.10990.20820.038-0.516-0.4457-0.6641-0.12560.00370.1588-0.26720.12340.50110.3994-0.0378-0.00940.50260.07580.49451.4569-34.1865-9.7648
27.4402-4.1756-4.22813.62312.85183.9264-0.11410.1858-0.5650.2566-0.11120.32460.3135-0.06570.19630.23110.0159-0.04250.22350.00230.3617-20.4577-29.4303-2.3904
32.36150.0776-0.19684.3603-0.1371.7256-0.0176-0.05580.2511-0.20440.11270.2663-0.2588-0.0722-0.10420.26890.0376-0.00150.2144-0.00310.2602-25.0447-10.0213-3.1535
42.1274-0.9934-0.27922.4070.41632.26750.09630.1809-0.0489-0.1671-0.10270.0085-0.05780.20480.00720.18960.0134-0.02090.2405-0.00470.2132-16.809-19.0674-5.5395
52.6608-1.1627-0.47576.07960.70424.086-0.44-0.4338-0.10991.10910.1969-0.04280.12130.4040.12770.34260.0646-0.02170.33980.03630.2162-17.7798-20.12377.2104
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 1971 )A0

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