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Yorodumi- PDB-6zsz: Crystal structure of the Grindelwald extracellular domain complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zsz | ||||||
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Title | Crystal structure of the Grindelwald extracellular domain complex | ||||||
Components | Protein grindelwald | ||||||
Keywords | SIGNALING PROTEIN / TNF receptor / JNK cascade / TNF / signaling / extracellular / tumor necrosis factor | ||||||
Function / homology | tumor 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 species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Palmerini, V. / Cecatiello, V. / Pasqualato, S. / Mapelli, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zsz.cif.gz | 30.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zsz.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zsz_validation.pdf.gz | 401.6 KB | Display | wwPDB validaton report |
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Full document | 6zsz_full_validation.pdf.gz | 401.6 KB | Display | |
Data in XML | 6zsz_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 6zsz_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zsz ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zsz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes pH 7.5, 45 % MPD, 0.2 M ammonium acetate concentration 82 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0751 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.0751 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→48.88 Å / Num. obs: 4051 / % possible obs: 96.4 % / Redundancy: 221.8 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 163.4 |
Reflection shell | Resolution: 1.92→5.21 Å / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 11.8 / Num. unique obs: 89 / CC1/2: 0.998 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.92→29.94 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 19.18 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.46 Å2 / Biso mean: 14.5752 Å2 / Biso min: 4.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→29.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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