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- PDB-5e9i: Crystal Structure of BAZ2B bromodomain in complex with fragment F60 -

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Basic information

Entry
Database: PDB / ID: 5e9i
TitleCrystal Structure of BAZ2B bromodomain in complex with fragment F60
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
1H-indol-6-ol / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 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 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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)13,6652
Polymers13,5321
Non-polymers1331
Water2,990166
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.030, 96.037, 57.902
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 2054-2168)
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-F60 / 1H-indol-6-ol


Mass: 133.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 4.27 Å3/Da / Density % sol: 71.16 %
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: 1.96→48.02 Å / Num. obs: 16565 / % possible obs: 97.2 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 32 / Num. measured all: 107292
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
1.96-2.016.90.3484.4821811910.9780.14199.6
8.98-48.0260.01381125921010.00698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→41.515 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 817 5.05 %
Rwork0.1883 15361 -
obs0.1897 16178 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.87 Å2 / Biso mean: 36.0265 Å2 / Biso min: 13.43 Å2
Refinement stepCycle: final / Resolution: 1.96→41.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 10 166 1123
Biso mean--27.98 42.73 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007985
X-RAY DIFFRACTIONf_angle_d1.0761327
X-RAY DIFFRACTIONf_chiral_restr0.038142
X-RAY DIFFRACTIONf_plane_restr0.005168
X-RAY DIFFRACTIONf_dihedral_angle_d13.997377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.08280.31991200.24072581X-RAY DIFFRACTION96
2.0828-2.24360.26871380.25072290X-RAY DIFFRACTION93
2.2436-2.46940.27661230.23532319X-RAY DIFFRACTION95
2.4694-2.82660.22781280.18572677X-RAY DIFFRACTION100
2.8266-3.56090.2071610.1832693X-RAY DIFFRACTION100
3.5609-41.5150.17961470.162801X-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)
18.9959-0.6105-4.0027-0.01070.35261.7264-0.697-0.9737-0.8491-0.12020.03810.1224-0.1950.3730.62830.3202-0.0225-0.01710.49550.1090.44521.5518-33.6733-9.7356
25.5672-5.2422-5.70384.89225.0815.9363-0.42480.1826-1.03330.23040.0050.74020.4873-0.06290.39280.26570.0073-0.00780.2340.00160.4212-20.722-29.4537-2.4275
35.66910.13090.41827.12991.87634.5488-0.1381-0.6178-0.14590.57840.52960.50340.0069-0.2538-0.16380.2230.06640.03730.26250.02310.2206-28.6793-18.66434.892
44.72941.27130.28844.53763.63982.9971-0.14930.2451.2087-1.05660.01921.4428-1.2497-0.8275-0.25240.4970.1493-0.05620.26530.02250.4476-30.0307-7.6712-5.3969
52.21531.58720.0072.0911.14011.39390.5040.24390.6578-0.2758-0.2775-0.1247-0.5834-0.1412-0.29440.3540.03310.10370.18710.03970.3319-20.7406-6.739-6.5201
64.4733-1.9656-0.1613.74060.36433.01820.15010.24720.0168-0.1479-0.1344-0.03080.03740.1980.01310.17490.0197-0.01430.15250.01760.1408-17.4135-18.9617-5.5536
74.4866-1.5173-1.15174.96610.40684.9851-0.5446-0.871-0.08920.71570.5331-0.12740.28480.516-0.02280.29110.0569-0.04240.32950.02530.1407-18.2687-19.79877.3383
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 1889 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1890 through 1900 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1901 through 1910 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1911 through 1943 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1944 through 1971 )A0

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