+Open data
-Basic information
Entry | Database: PDB / ID: 1b0v | ||||||||||||
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Title | I40N MUTANT OF AZOTOBACTER VINELANDII FDI | ||||||||||||
Components | PROTEIN (FERREDOXIN) | ||||||||||||
Keywords | ELECTRON TRANSPORT / IRON-SULFUR | ||||||||||||
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: 2.8 Å | ||||||||||||
Authors | Sridhar, V. / Prasad, G.S. / Stout, C.D. / Chen, K. / Burgess, B.K. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I. Authors: Chen, K. / Tilley, G.J. / Sridhar, V. / Prasad, G.S. / Stout, C.D. / Armstrong, F.A. / 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 | 1b0v.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0v.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b0v_validation.pdf.gz | 420.7 KB | Display | wwPDB validaton report |
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Full document | 1b0v_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 1b0v_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1b0v_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0v ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0v | HTTPS FTP |
-Related structure data
Related structure data | 6fd1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12060.476 Da / Num. of mol.: 4 / Mutation: I40N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: JG100 / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P00214 #2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-F3S / Compound details | 4 COPIES OF I40N FDI IN THE ASYMMETRIC UNIT, EACH WITH A DIFFERENT CONFORMATION OF ASN40. THIS ...4 COPIES OF I40N FDI IN THE ASYMMETRIC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 55 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: Shen, B., (1994) J. Biol. Chem., 269, 8564. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 11184 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rsym value: 0.165 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.2 / % possible all: 53 |
Reflection | *PLUS Num. obs: 11182 / Num. measured all: 17912 / Rmerge(I) obs: 0.165 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FD1 Resolution: 2.8→20 Å / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 0
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Displacement parameters | Biso mean: 26.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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