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Yorodumi- PDB-1jfu: CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF TLPA FROM BRADYRHIZOBI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jfu | ||||||
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Title | CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF TLPA FROM BRADYRHIZOBIUM JAPONICUM | ||||||
Components | THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA | ||||||
Keywords | MEMBRANE PROTEIN / THIOREDOXIN-LIKE / DOUBLE DISULFIDE BRIDGE | ||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.6 Å | ||||||
Authors | Capitani, G. / Rossmann, R. / Sargent, D.F. / Gruetter, M.G. / Richmond, T.J. / Hennecke, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Structure of the soluble domain of a membrane-anchored thioredoxin-like protein from Bradyrhizobium japonicum reveals unusual properties. Authors: Capitani, G. / Rossmann, R. / Sargent, D.F. / Grutter, M.G. / Richmond, T.J. / Hennecke, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jfu.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfu.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfu ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfu | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19788.889 Da / Num. of mol.: 2 / Fragment: SOLUBLE DOMAIN OF TLPA (RESIDUES 36-221) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: TLPA / Plasmid: PMAL-P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43221 #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: 1.99 Å3/Da / Density % sol: 38.28 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Bicine, NaCl, PEG550 MME, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 7 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1999 / Details: OSMIC Confocal Max-Flux |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→15 Å / Num. obs: 36890 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.6→1.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3346 / % possible all: 64 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.6→15 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 19.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.181 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.3 Å2 | |||||||||||||||||||||
Refine LS restraints | *PLUS
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