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Yorodumi- PDB-7sr1: Crystal structure of the human SNX25 regulator of G-protein signa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sr1 | |||||||||
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Title | Crystal structure of the human SNX25 regulator of G-protein signalling (RGS) domain | |||||||||
Components | Sorting nexin-25 | |||||||||
Keywords | SIGNALING PROTEIN / endosome / sorting nexin / SNX / RGS / SNX25 / lipid droplet | |||||||||
Function / homology | Function and homology information phosphatidylinositol binding / negative regulation of transforming growth factor beta receptor signaling pathway / membrane => GO:0016020 / intracellular membrane-bounded organelle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Collins, B.M. / Paul, B. / Weeratunga, S. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Front Cell Dev Biol / Year: 2022 Title: Structural Predictions of the SNX-RGS Proteins Suggest They Belong to a New Class of Lipid Transfer Proteins. Authors: Paul, B. / Weeratunga, S. / Tillu, V.A. / Hariri, H. / Henne, W.M. / Collins, B.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sr1.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sr1.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 7sr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/7sr1 ftp://data.pdbj.org/pub/pdb/validation_reports/sr/7sr1 | HTTPS FTP |
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-Related structure data
Related structure data | 7sr2C 2bv1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 15115.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX25 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A494C0S0 #2: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 57.61 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.006 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.84 Å / Num. obs: 13200 / % possible obs: 96.27 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.03 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.061 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1000 / CC1/2: 0.718 / Rpim(I) all: 0.467 / % possible all: 73.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BV1 Resolution: 2.4→45.84 Å / SU ML: 0.3459 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.028 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 51.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.84 Å
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Refine LS restraints |
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LS refinement shell |
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