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Yorodumi- PDB-2x8x: Structure of the N-terminal domain of Omp85 from the Thermophilic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x8x | ||||||
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Title | Structure of the N-terminal domain of Omp85 from the Thermophilic Cyanobacterium Thermosynechococcus elongatus | ||||||
Components | TLR1789 PROTEIN | ||||||
Keywords | CHAPERONE / TOC75 / PROTEIN TARGETING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THERMOSYNECHOCOCCUS ELONGATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å | ||||||
Authors | Arnold, T. / Zeth, K. / Linke, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Omp85 from the Thermophilic Cyanobacterium Thermosynechococcus Elongatus Differs from Proteobacterial Omp85 in Structure and Domain Composition. Authors: Arnold, T. / Zeth, K. / Linke, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x8x.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x8x.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x8x ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x8x | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26293.779 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 86-320 Source method: isolated from a genetically manipulated source Details: CONTAINS THREE POTRA DOMAINS Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DI03 |
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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: 3.14 Å3/Da / Density % sol: 60.78 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 4000, 0.8M LiCl, 0.1M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESERACH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→2 Å / Num. obs: 21967 / % possible obs: 90.9 % / Observed criterion σ(I): 3 / Redundancy: 42 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.66 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 44 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.97→24.41 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.083 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.475 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→24.41 Å
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