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Yorodumi- PDB-4uc2: Crystal structure of translocator protein 18kDa (TSPO) from rhodo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uc2 | ||||||
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Title | Crystal structure of translocator protein 18kDa (TSPO) from rhodobacter sphaeroides (A139T mutant) in P212121 space group | ||||||
Components | TRANSLOCATOR PROTEIN TSPO | ||||||
Keywords | MEMBRANE PROTEIN / mitochondria / transport / transmembrane protein | ||||||
Function / homology | Function and homology information tetrapyrrole metabolic process / tetrapyrrole binding / lipid binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Li, F. / Liu, J. / Zheng, Y. / Garavito, R.M. / Ferguson-Miller, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2015 Title: Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism. Authors: Li, F. / Liu, J. / Zheng, Y. / Garavito, R.M. / Ferguson-Miller, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uc2.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uc2.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uc2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4uc2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4uc2_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 4uc2_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/4uc2 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/4uc2 | HTTPS FTP |
-Related structure data
Related structure data | 4uc1SC 4uc3C 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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Unit cell |
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-Components
#1: Protein | Mass: 17812.791 Da / Num. of mol.: 2 / Mutation: A139T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RFC8 #2: Chemical | ChemComp-OLC / ( #3: Chemical | ChemComp-PG4 / | #4: 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: 2.78 Å3/Da / Density % sol: 55.78 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8.5 Details: 23% PEG 3350, 0.1 M (NH4)2SO4 and 0.1 M Hepes buffer pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.003 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.003 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.65 Å / Num. obs: 29986 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.36 Å2 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UC1 Resolution: 2.4→43.65 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
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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: 84.81 Å2 / Biso mean: 42.4165 Å2 / Biso min: 16.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→43.65 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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