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

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Entry
Database: PDB / ID: 5cqa
TitleCrystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide (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 / regulation of transcription by RNA polymerase II / DNA binding / metal 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2LY / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 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 N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide (SGC - ...Title: Crystal structure of the second bromodomain of bromodomain adjancent to zinc finger domain protein 2B (BAZ2B) in complex with N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide (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)13,6943
Polymers13,4321
Non-polymers2612
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint3 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.160, 96.940, 58.110
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: 13432.443 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1858-1970
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
#2: Chemical ChemComp-2LY / N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide


Mass: 199.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / 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: 4.56 Å3/Da / Density % sol: 73.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG6000 , 10% ethylene glycol , 0.1M MES pH 6.0 , 0.1M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 2.13→37.22 Å / Num. obs: 13238 / % possible obs: 98.4 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.067 / Net I/σ(I): 16.3 / Num. measured all: 83872
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.13-2.196.30.7923.259859550.7130.34498.5
9.53-37.225.80.03449.410191770.9990.01597.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→37.2 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 662 5.01 %
Rwork0.1753 --
obs0.1776 13223 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.65 Å2 / Biso mean: 30.6952 Å2 / Biso min: 15.71 Å2
Refinement stepCycle: final / Resolution: 2.13→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 17 166 1110
Biso mean--37.37 38.02 -
Num. residues----115

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