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Yorodumi- PDB-7wf8: Crystal structure of mouse SNX25 RGS domain in space group P212121 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wf8 | ||||||
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Title | Crystal structure of mouse SNX25 RGS domain in space group P212121 | ||||||
Components | Sorting nexin-25 | ||||||
Keywords | PROTEIN TRANSPORT / Sorting nexin / SNX25 / RGS | ||||||
Function / homology | Function and homology information receptor catabolic process / type I transforming growth factor beta receptor binding / phosphatidylinositol binding / negative regulation of transforming growth factor beta receptor signaling pathway / protein transport / endosome membrane / endosome Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Zhang, Y. / Xu, J. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2022 Title: Structural Studies Reveal Unique Non-canonical Regulators of G Protein Signaling Homology (RH) Domains in Sorting Nexins. Authors: Zhang, Y. / Chen, R. / Dong, Y. / Zhu, J. / Su, K. / Liu, J. / Xu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wf8.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wf8.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wf8_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7wf8_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 7wf8_validation.xml.gz | 16 KB | Display | |
Data in CIF | 7wf8_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/7wf8 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/7wf8 | HTTPS FTP |
-Related structure data
Related structure data | 7wf6C 7wf9C 1zv4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15763.890 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3ZT31 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1M Tris pH 8.5, 25% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.35→52.42 Å / Num. obs: 68289 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.025 / Rrim(I) all: 0.073 / Net I/σ(I): 13.5 / Num. measured all: 553629 / Scaling rejects: 367 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZV4 Resolution: 1.35→48.99 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.899 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0489 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.96 Å2 / Biso mean: 19.504 Å2 / Biso min: 10.46 Å2
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Refinement step | Cycle: final / Resolution: 1.35→48.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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