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- PDB-2a90: Crystal Structure of the tandem WWE domain of Drosophila Deltex -

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Basic information

Entry
Database: PDB / ID: 2a90
TitleCrystal Structure of the tandem WWE domain of Drosophila Deltex
ComponentsDeltex protein
KeywordsMETAL BINDING PROTEIN / WWE domain
Function / homology
Function and homology information


Activated NOTCH1 Transmits Signal to the Nucleus / wing disc development / Notch receptor processing / Notch binding / positive regulation of Notch signaling pathway / negative regulation of Notch signaling pathway / Notch signaling pathway / RING-type E3 ubiquitin transferase / SH3 domain binding / endocytosis ...Activated NOTCH1 Transmits Signal to the Nucleus / wing disc development / Notch receptor processing / Notch binding / positive regulation of Notch signaling pathway / negative regulation of Notch signaling pathway / Notch signaling pathway / RING-type E3 ubiquitin transferase / SH3 domain binding / endocytosis / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #50 / Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / Signal recognition particle alu RNA binding heterodimer, srp9/1 / WWE domain / WWE domain superfamily ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #50 / Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / Signal recognition particle alu RNA binding heterodimer, srp9/1 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsZweifel, M.E. / Leahy, D.J. / Barrick, D.
CitationJournal: Structure / Year: 2005
Title: Structure and Notch Receptor Binding of the Tandem WWE Domain of Deltex.
Authors: Zweifel, M.E. / Leahy, D.J. / Barrick, D.
History
DepositionJul 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE The cysteines at residue positions 47, 155, 171 and 184 were converted to serines by site- ...SEQUENCE The cysteines at residue positions 47, 155, 171 and 184 were converted to serines by site-directed mutagenesis in the construct. These substitutions do not correspond to known mutations in the Deltex protein, but were made to improve the solubility and long-term stability of the polypeptide.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deltex protein


Theoretical massNumber of molelcules
Total (without water)26,8131
Polymers26,8131
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.760, 57.760, 80.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Deltex protein


Mass: 26813.234 Da / Num. of mol.: 1 / Fragment: WWE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dx / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q23985
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795, 0.9793, 0.9724
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2004
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.97241
ReflectionResolution: 2.15→40.8 Å / Num. obs: 27871
Reflection shellResolution: 2.15→2.28 Å / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→40.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The sf file of this entry contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1300 4.6 %RANDOM
Rwork0.23 ---
all-28099 --
obs-26923 95.8 %-
Solvent computationBsol: 56.987 Å2
Displacement parametersBiso mean: 55.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.803 Å20 Å20 Å2
2---0.803 Å20 Å2
3---1.607 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 54 1340
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 204 4.9 %
Rwork0.312 3957 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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