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Yorodumi- PDB-1uj8: Structures of ORF3 in Two Crystal Forms, a Member of Isc Machiner... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uj8 | ||||||
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Title | Structures of ORF3 in Two Crystal Forms, a Member of Isc Machinery of E. coli Involved in the Assembly of Iron-Sulfur Clusters | ||||||
Components | Hypothetical protein yfhJ | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / IRON-SULFUR CLUSTER / ISC | ||||||
Function / homology | Function and homology information enzyme inhibitor activity / iron-sulfur cluster assembly / ferrous iron binding / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Shimomura, Y. / Takahashi, Y. / Fukuyama, K. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of Escherichia coli YfhJ protein, a member of the ISC machinery involved in assembly of iron-sulfur clusters. Authors: Shimomura, Y. / Takahashi, Y. / Kakuta, Y. / Fukuyama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uj8.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uj8.ent.gz | 18.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uj8_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
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Full document | 1uj8_full_validation.pdf.gz | 419.7 KB | Display | |
Data in XML | 1uj8_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1uj8_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1uj8 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1uj8 | HTTPS FTP |
-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
#1: Protein | Mass: 9011.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P0C0L9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→20 Å / Num. obs: 7922 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.224 / Num. unique all: 795 / Rsym value: 0.224 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→19.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 953146.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.0279 Å2 / ksol: 0.464872 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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