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Yorodumi- PDB-1fdn: REFINED CRYSTAL STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CLOSTR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fdn | ||||||
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Title | REFINED CRYSTAL STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDURICI AT 1.84 ANGSTROMS RESOLUTION | ||||||
Components | FERREDOXIN | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium acidurici (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.84 Å | ||||||
Authors | Duee, E. / Fanchon, E. / Vicat, J. / Sieker, L.C. / Meyer, J. / Moulis, J-M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution. Authors: Duee, E.D. / Fanchon, E. / Vicat, J. / Sieker, L.C. / Meyer, J. / Moulis, J.M. #1: Journal: Biochem.J. / Year: 1993 Title: Sequences of Clostridial Ferredoxins Authors: Meyer, J. / Moulis, J.-M. / Scherrer, N. / Gagnon, J. / Ulrich, J. #2: Journal: J.Biol.Chem. / Year: 1988 Title: Crystal Structure of Clostridium Acidi-Urici Ferredoxin at 5 Angstroms Resolution Based on Measurements of Anomalous X-Ray Scattering at Multiple Wavelengths Authors: Krishnamurthy, H.M. / Hendrickson, W.A. / Orme-Johnson, W.H. / Merritt, E.A. / Phizackerley, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fdn.cif.gz | 22 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fdn.ent.gz | 14 KB | Display | PDB format |
PDBx/mmJSON format | 1fdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fdn ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fdn | 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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Atom site foot note | 1: TWO ALTERNATE POSITIONS FOR THE SIDE CHAIN OF ASN 21 HAVE BEEN OBSERVED AND GIVEN OCCUPANCIES OF 0.5. 2: THE EXACT POSITIONS OF ASP 27 AND ASP 28 ARE UNDEFINED FROM THE X-RAY DATA. THESE RESIDUES HAVE BEEN BUILT WITH A GOOD GEOMETRY FOR THE MAIN CHAIN AND REASONABLE CHI ANGLES FOR THE SIDE CHAINS. |
-Components
#1: Protein | Mass: 5540.179 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acidurici (bacteria) / References: UniProt: P00198 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.49 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 281 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 4203 / % possible obs: 92 % / Num. measured all: 15645 / Rmerge F obs: 0.062 |
-Processing
Software |
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Refinement | Resolution: 1.84→18 Å / σ(F): 2 Details: THE EXACT POSITIONS OF ASP 27 AND ASP 28 ARE UNDEFINED FROM THE X-RAY DATA. THESE RESIDUES HAVE BEEN BUILT WITH A GOOD GEOMETRY FOR THE MAIN CHAIN AND REASONABLE CHI ANGLES FOR THE SIDE CHAINS.
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Refinement step | Cycle: LAST / Resolution: 1.84→18 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.58 |