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- PDB-5dyx: Crystal Structure of BAZ2B bromodomain in complex with fragment F59 -

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Basic information

Entry
Database: PDB / ID: 5dyx
TitleCrystal Structure of BAZ2B bromodomain in complex with fragment F59
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 / 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
ADENINE / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionSep 25, 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)13,6672
Polymers13,5321
Non-polymers1351
Water2,288127
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint3 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.129, 96.236, 57.783
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
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 70.49 %
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 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→48.12 Å / Num. obs: 19634 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Net I/σ(I): 11.8 / Num. measured all: 126337 / Scaling rejects: 23
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
1.85-1.896.30.7332.2731911540.8650.31299.6
9.06-48.125.70.08222.811512010.9940.03599.2

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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
Starting model: 4IR5

4ir5


Resolution: 1.85→42.28 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 990 5.05 %
Rwork0.1761 18618 -
obs0.1774 19608 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.37 Å2 / Biso mean: 44.0179 Å2 / Biso min: 21.47 Å2
Refinement stepCycle: final / Resolution: 1.85→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 10 127 1084
Biso mean--48.57 48.64 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007979
X-RAY DIFFRACTIONf_angle_d11317
X-RAY DIFFRACTIONf_chiral_restr0.036141
X-RAY DIFFRACTIONf_plane_restr0.004166
X-RAY DIFFRACTIONf_dihedral_angle_d14.21373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.94760.30311560.26862573X-RAY DIFFRACTION99
1.9476-2.06960.25431480.21532620X-RAY DIFFRACTION100
2.0696-2.22940.19871170.19192652X-RAY DIFFRACTION100
2.2294-2.45370.22831350.18772641X-RAY DIFFRACTION100
2.4537-2.80870.23511440.18492659X-RAY DIFFRACTION100
2.8087-3.53840.21651330.18752695X-RAY DIFFRACTION100
3.5384-42.280.16591570.15012778X-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)
10.1054-0.2322-0.23860.35570.35940.0559-0.6622-0.6861-0.3645-0.3334-0.04110.2459-0.2530.4186-0.01050.3324-0.0128-0.01920.56890.06390.55351.4525-34.4542-9.8532
20.1254-0.05880.06450.0912-0.02490.035-0.24340.1833-0.85470.32010.05910.47120.6401-0.1787-0.00040.33790.0363-0.01810.30540.00620.4871-20.4322-29.4155-2.3438
30.77-0.380.39220.52460.3070.3746-0.0802-0.15880.2823-0.08590.07330.1804-0.25220.01130.00020.34340.05370.03210.26560.00390.337-25.0915-10.0669-3.1089
41.0787-0.60.25730.6904-0.24040.38240.14650.18420.054-0.1165-0.14940.0349-0.15640.187600.27080.0287-0.02820.3-0.02020.25-16.747-19.0945-5.561
50.15820.11850.21940.2418-0.10590.8124-0.5346-0.6287-0.12591.0210.4131-0.0141-0.0270.2995-0.00090.44770.1295-0.00180.37640.02560.2741-17.6948-20.08857.2337
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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