+Open data
-Basic information
Entry | Database: PDB / ID: 1g3o | ||||||
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Title | CRYSTAL STRUCTURE OF V19E MUTANT OF FERREDOXIN I | ||||||
Components | 7FE FERREDOXIN I | ||||||
Keywords | ELECTRON TRANSPORT / Iron-sulfur clusters / ferredoxin | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Stout, C.D. / Burgess, B.K. / Bonagura, C.A. / Jung, Y.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential Authors: Chen, K. / Jung, Y.S. / Bonagura, C.A. / Tilley, G.J. / Prasad, G.S. / Sridhar, V. / Armstrong, F.A. / Stout, C.D. / 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 | 1g3o.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3o.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 1g3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g3o_validation.pdf.gz | 394.3 KB | Display | wwPDB validaton report |
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Full document | 1g3o_full_validation.pdf.gz | 397.1 KB | Display | |
Data in XML | 1g3o_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1g3o_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3o ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3o | HTTPS FTP |
-Related structure data
Related structure data | 1g6bC 1gaoC 7fd1S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 12089.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MUTANT DESIGNED TO TEST REDUCTION POTENTIAL SHIFT / Source: (natural) Azotobacter vinelandii (bacteria) / 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.39 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: Ammonium sulfate, tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Details: Shen, B., (1994) J. Biol. Chem., 269, 8564. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: focussing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 17756 / Num. obs: 17756 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.468 / % possible all: 98.6 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7FD1 Resolution: 1.65→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: X-plor 3.8
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Displacement parameters | Biso mean: 20.3 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 6.4 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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