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Yorodumi- PDB-1f37: STRUCTURE OF A THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN FROM AQUIFEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f37 | ||||||
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Title | STRUCTURE OF A THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN FROM AQUIFEX AEOLICUS | ||||||
Components | FERREDOXIN [2FE-2S] | ||||||
Keywords | ELECTRON TRANSPORT / ferredoxin / [2Fe-2S] cluster / thioredoxin fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Yeh, A.P. / Chatelet, C. / Soltis, S.M. / Kuhn, P. / Meyer, J. / Rees, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structure of a thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus. Authors: Yeh, A.P. / Chatelet, C. / Soltis, S.M. / Kuhn, P. / Meyer, J. / Rees, D.C. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 1999 Title: A [2Fe-2S] protein from the hyperthermophilic bacterium Aquifex aeolicus Authors: Chatelet, C. / Gaillard, J. / Petillot, Y. / Louwagie, M. / Meyer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f37.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f37.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f37 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f37 | 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 on special symmetry positions |
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Details | The biological assembly is a homodimer |
-Components
#1: Protein | Mass: 12206.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O66511 #2: Chemical | #3: Chemical | #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: 2.43 Å3/Da / Density % sol: 49.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: ammonium sulfate, p-dioxane, 2-(N-morpholino)-ethane sulfonic acid, pH 6.5, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. all: 11218 / Num. obs: 11218 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.8 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.277 / Num. unique all: 550 / % possible all: 99.8 | |||||||||||||||||||||||||
Reflection | *PLUS Num. measured all: 74834 | |||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 99.8 % / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Resolution: 2.3→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The data that was used in the refinement was collected at a wavelength of 1.5001 Angstroms. Due to the iron anomalous signal resulting from collecting at this wavelength, the structure was ...Details: The data that was used in the refinement was collected at a wavelength of 1.5001 Angstroms. Due to the iron anomalous signal resulting from collecting at this wavelength, the structure was refined against the separate Friedel mates. The reported number of reflections used in the refinement counts each mate of a Friedel pair as a separate reflection.
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Refinement step | Cycle: LAST / Resolution: 2.3→500 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 7.5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |