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- PDB-5cq6: Crystal structure of the bromodomain of bromodomain adjacent to z... -

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Basic information

Entry
Database: PDB / ID: 5cq6
TitleCrystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with 2,6-Pyridinedicarboxylic 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 / 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
PYRIDINE-2,6-DICARBOXYLIC ACID / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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 2,6-Pyridinedicarboxylic 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

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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)14,5165
Polymers14,0571
Non-polymers4584
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint8 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.845, 96.600, 58.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2118-

HOH

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Components

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


Mass: 14057.129 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1858-1972
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID / Dipicolinic acid


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.05 Å3/Da / Density % sol: 69.64 %
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 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.9871
ReflectionResolution: 1.97→29.17 Å / Num. obs: 16453 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Net I/σ(I): 15.9 / Num. measured all: 106277 / Scaling rejects: 1
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
1.97-2.025.90.8092.1664111290.790.35493.6
8.8-29.176.10.02957.613332170.9990.01397.6

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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: 1.97→19.535 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 763 4.65 %
Rwork0.1898 --
obs0.1914 16420 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.48 Å2 / Biso mean: 31.7177 Å2 / Biso min: 18.55 Å2
Refinement stepCycle: final / Resolution: 1.97→19.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 32 131 1093
Biso mean--43.88 38.38 -
Num. residues----115

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