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- PDB-6zsy: Crystal structure of the Grindelwald extracellular domain complex -

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Basic information

Entry
Database: PDB / ID: 6zsy
TitleCrystal structure of the Grindelwald extracellular domain complex
ComponentsProtein grindelwald
KeywordsSIGNALING PROTEIN / TNF receptor / JNK cascade / TNF / signaling / extracellular / tumor necrosis factor
Function / homologytumor necrosis factor receptor activity / positive regulation of programmed cell death / negative regulation of reactive oxygen species biosynthetic process / tumor necrosis factor-mediated signaling pathway / positive regulation of JNK cascade / apical plasma membrane / plasma membrane / Protein grindelwald
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.926 Å
AuthorsPalmerini, V. / Cecatiello, V. / Pasqualato, S. / Mapelli, M.
CitationJournal: Nat Commun / Year: 2021
Title: Drosophila TNFRs Grindelwald and Wengen bind Eiger with different affinities and promote distinct cellular functions.
Authors: Palmerini, V. / Monzani, S. / Laurichesse, Q. / Loudhaief, R. / Mari, S. / Cecatiello, V. / Olieric, V. / Pasqualato, S. / Colombani, J. / Andersen, D.S. / Mapelli, M.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: Protein grindelwald


Theoretical massNumber of molelcules
Total (without water)5,9201
Polymers5,9201
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.483, 31.483, 97.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

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Components

#1: Protein Protein grindelwald


Mass: 5919.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: grnd, CG10176 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VJ83
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na-Hepes pH 7.5, 45 % MPD, 0.2 M Ammonium Acetate concentration 82 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 0.926→29.967 Å / Num. obs: 33869 / % possible obs: 98.2 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.5
Reflection shellResolution: 0.926→0.942 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3 / Num. unique obs: 1382 / CC1/2: 0.849 / % possible all: 83.8

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Processing

Software
NameClassification
SHELXrefinement
autoPROCdata collection
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 0.926→29.967 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1571 1684 -
Rwork0.1296 --
obs-33869 98.15 %
Displacement parametersBiso max: 87.17 Å2 / Biso mean: 16.4936 Å2 / Biso min: 6.02 Å2
Refinement stepCycle: LAST / Resolution: 0.926→29.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms379 0 0 83 462

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