+Open data
-Basic information
Entry | Database: PDB / ID: 8gn9 | ||||||
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Title | SPFH domain of Pyrococcus horikoshii stomatin | ||||||
Components | Stomatin homolog PH1511 | ||||||
Keywords | MEMBRANE PROTEIN / mixed alpha-beta / dimer / scaffolding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Komatsu, T. / Matsui, I. / Yokoyama, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem Biophys Rep / Year: 2022 Title: Structural and mutational studies suggest key residues to determine whether stomatin SPFH domains form dimers or trimers. Authors: Komatsu, T. / Matsui, I. / Yokoyama, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gn9.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gn9.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gn9_validation.pdf.gz | 422 KB | Display | wwPDB validaton report |
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Full document | 8gn9_full_validation.pdf.gz | 422.4 KB | Display | |
Data in XML | 8gn9_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 8gn9_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/8gn9 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/8gn9 | HTTPS FTP |
-Related structure data
Related structure data | 3bk6S S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 12283.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residues 63-170 / Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1511 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: O59180 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M sodium acetate, 50 mM Tris-HCl, 15% PEG4000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 3909 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 31.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 536 / CC1/2: 0.951 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3bk6 Resolution: 2.5→19.81 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.938 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.362 / 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: 91.89 Å2 / Biso mean: 43.406 Å2 / Biso min: 25.56 Å2
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Refinement step | Cycle: final / Resolution: 2.5→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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