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- PDB-5e9k: Crystal Structure of BAZ2B bromodomain in complex with fragment F275 -

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Basic information

Entry
Database: PDB / ID: 5e9k
TitleCrystal Structure of BAZ2B bromodomain in complex with fragment F275
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
2-chloro-1H-imidazole / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.067 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)13,6342
Polymers13,5321
Non-polymers1031
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.331, 96.181, 57.794
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-5KX / 2-chloro-1H-imidazole


Mass: 102.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3ClN2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.18 Å3/Da / Density % sol: 70.55 %
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: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.067→48.09 Å / Num. all: 14219 / Num. obs: 14219 / % possible obs: 99.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 31.71 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.054 / Rsym value: 0.048 / Net I/av σ(I): 12.407 / Net I/σ(I): 26.3 / Num. measured all: 121784
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.067-2.188.50.3961.91715020120.1510.3966.197.8
2.18-2.318.30.2692.81630319550.1050.2698.699.9
2.31-2.478.20.1933.91473318030.0750.19310.5100
2.47-2.678.80.1315.81507517160.0490.13114.9100
2.67-2.929.20.089.41444715680.0290.0823.1100
2.92-3.279.10.05413.41295714290.020.05432100
3.27-3.778.60.035181100912730.0140.03547.699.9
3.77-4.627.60.02623.4830010860.0110.02658.6100
4.62-6.538.70.0242675278690.0090.02463.8100
6.53-48.098.40.0212842835080.0080.02176.299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR5

4ir5


Resolution: 2.067→48.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 1342 5.04 %
Rwork0.1942 25280 -
obs0.1955 14219 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.09 Å2 / Biso mean: 49.5496 Å2 / Biso min: 30.52 Å2
Refinement stepCycle: final / Resolution: 2.067→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 6 65 1018
Biso mean--45.63 50.2 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007981
X-RAY DIFFRACTIONf_angle_d1.0771320
X-RAY DIFFRACTIONf_chiral_restr0.038142
X-RAY DIFFRACTIONf_plane_restr0.004168
X-RAY DIFFRACTIONf_dihedral_angle_d13.49378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0665-2.14040.32721280.28872441X-RAY DIFFRACTION94
2.1404-2.22610.2761310.2632514X-RAY DIFFRACTION99
2.2261-2.32740.26721310.25062522X-RAY DIFFRACTION99
2.3274-2.45010.26031330.2282517X-RAY DIFFRACTION100
2.4501-2.60360.2731390.22522556X-RAY DIFFRACTION100
2.6036-2.80460.19321360.20822534X-RAY DIFFRACTION100
2.8046-3.08680.26161320.21012552X-RAY DIFFRACTION100
3.0868-3.53340.25121390.21582548X-RAY DIFFRACTION100
3.5334-4.45120.18871370.16462543X-RAY DIFFRACTION100
4.4512-48.090.16091360.14772553X-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)
12.8384-0.1690.216-0.0054-0.1102-0.0253-0.5178-0.69750.53280.05050.0002-0.03930.3203-0.19560.51890.3926-0.0297-0.00350.6332-0.04950.5843-1.352734.3013-9.6453
26.531-3.23353.92533.1929-2.2874.6301-0.12850.12670.25970.2836-0.0018-0.2237-0.28880.23550.10310.298-0.00570.04980.3179-0.00440.386420.48229.4867-2.2624
32.5508-0.07710.17592.46920.2632.86690.08610.1072-0.1072-0.0583-0.059-0.12720.4897-0.0362-0.05720.35750.02320.0180.321-0.00440.329220.630314.9628-4.3879
42.8462-0.56490.13544.297-0.12472.7307-0.3736-0.5530.09920.97150.26480.16320.0756-0.30580.02670.42590.07740.04770.4366-0.02690.316217.738119.66437.3286
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 1943 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1944 through 1971 )A0

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