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- PDB-5cq3: Crystal structure of the bromodomain of bromodomain adjacent to z... -

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Basic information

Entry
Database: PDB / ID: 5cq3
TitleCrystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with 6-Hydroxypicolinic acid (SGC - Diamond I04-1 fragment screening)
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC
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
6-hydroxypyridine-2-carboxylic acid / PHOSPHATE ION / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.925 Å
AuthorsBradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of the second bromodomain of bromodomain adjancent to zinc finger domain protein 2B (BAZ2B) in complex with 6-Hydroxypicolinic acid (SGC - Diamond I04-1 fragment screening)
Authors: Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1May 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)14,4936
Polymers14,0571
Non-polymers4365
Water2,594144
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-1 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.511, 97.030, 58.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 14057.129 Da / Num. of mol.: 1 / Fragment: Bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pNIC28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8

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Non-polymers , 5 types, 149 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-53B / 6-hydroxypyridine-2-carboxylic acid


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 4.04 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% PEG600 , 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.92→29.1 Å / Num. obs: 17474 / % possible obs: 98.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.034 / Net I/σ(I): 14.2 / Num. measured all: 112657
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
1.92-1.975.80.8412662911510.8610.36889.2
8.6-29.16.10.03939.213932280.9980.01697.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.925→19.568 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 760 4.36 %
Rwork0.1999 --
obs0.2017 17446 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.35 Å2 / Biso mean: 37.2228 Å2 / Biso min: 20.22 Å2
Refinement stepCycle: final / Resolution: 1.925→19.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 43 144 1117
Biso mean--48.67 43.18 -
Num. residues----115

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