+Open data
-Basic information
Entry | Database: PDB / ID: 1xer | ||||||
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Title | STRUCTURE OF FERREDOXIN | ||||||
Components | FERREDOXIN | ||||||
Keywords | ELECTRON TRANSPORT / IRON-SULFUR / DUPLICATION | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii str. 7 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2 Å | ||||||
Authors | Fujii, T. / Hata, Y. / Moriyama, H. / Wakagi, T. / Tanaka, N. / Oshima, T. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Novel zinc-binding centre in thermoacidophilic archaeal ferredoxins. Authors: Fujii, T. / Hata, Y. / Wakagi, T. / Tanaka, N. / Oshima, T. #1: Journal: J.Biochem.(Tokyo) / Year: 1991 Title: Crystallization and Preliminary X-Ray Studies on Sulfolobus Acidocaldarius Ferredoxin Authors: Fujii, T. / Moriyama, H. / Takenaka, A. / Tanaka, N. / Wakagi, T. / Oshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xer.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xer.ent.gz | 21.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/1xer ftp://data.pdbj.org/pub/pdb/validation_reports/xe/1xer | 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
#1: Protein | Mass: 11026.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus tokodaii str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: STRAIN 7 / References: UniProt: P55907 | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | BECAUSE OF THE ELECTRON DENSITY OF THE SIDE CHAIN OF LYS 29 IS NOT CLEAR, THE EXACT POSITION OF THE ...BECAUSE OF THE ELECTRON DENSITY OF THE SIDE CHAIN OF LYS 29 IS NOT CLEAR, THE EXACT POSITION OF THE SIDE CHAIN OF LYS 29 IS UNDEFINED. ALTHOUGH IT IS KNOWN FROM CHEMICAL ANALYSIS THAT THE N-ZETA ATOM OF LYS 29 IS MONOMETHYL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 33 % |
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Crystal grow | *PLUS Method: batch method |
Components of the solutions | *PLUS Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 24, 1992 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→35.59 Å / Num. obs: 8689 / % possible obs: 86 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2→8 Å / σ(F): 3
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Displacement parameters | Biso mean: 13.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.22 |