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Yorodumi- PDB-1frm: AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SUR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1frm | ||||||
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Title | AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL | ||||||
Components | FERREDOXIN | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Stout, C.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Azotobacter vinelandii ferredoxin I. Alteration of individual surface charges and the [4FE-4S]2+/+ cluster reduction potential. Authors: Shen, B. / Jollie, D.R. / Stout, C.D. / Diller, T.C. / Armstrong, F.A. / Gorst, C.M. / La Mar, G.N. / Stephens, P.J. / Burgess, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1frm.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1frm.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 1frm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1frm_validation.pdf.gz | 396.1 KB | Display | wwPDB validaton report |
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Full document | 1frm_full_validation.pdf.gz | 397 KB | Display | |
Data in XML | 1frm_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1frm_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1frm ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1frm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12001.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: POTENTIAL / Plasmid: PKT230 / References: UniProt: P00214 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-F3S / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.41 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 55 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: Stout, C.D., (1979) J. Biol. Chem., 254, 3598. | |||||||||||||||||||||||||
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 | Num. obs: 8094 / % possible obs: 78.8 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 40698 / Rmerge F obs: 0.078 |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 18.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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