+Open data
-Basic information
Entry | Database: PDB / ID: 1b13 | ||||||
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Title | CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10A MUTANT | ||||||
Components | PROTEIN (RUBREDOXIN) | ||||||
Keywords | ELECTRON TRANSPORT / METALLOPROTEIN / IRON SULFUR / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.5 Å | ||||||
Authors | Maher, M.J. / Guss, J.M. / Wilce, M.C.J. / Wedd, A.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert. Authors: Maher, M.J. / Xiao, Z. / Wilce, M.C. / Guss, J.M. / Wedd, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b13.cif.gz | 22.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b13.ent.gz | 13.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b13_validation.pdf.gz | 350.7 KB | Display | wwPDB validaton report |
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Full document | 1b13_full_validation.pdf.gz | 350.6 KB | Display | |
Data in XML | 1b13_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 1b13_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/1b13 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/1b13 | HTTPS FTP |
-Related structure data
Related structure data | 1b2jC 1b2oC 5rxnS 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: 6065.637 Da / Num. of mol.: 1 / Mutation: G10A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Strain: JM109 / Cellular location: CYTOPLASM / Gene: CLORUB / Plasmid: PKK223-3 / Gene (production host): CLORUB / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00268 |
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#2: Chemical | ChemComp-FE / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4.6. | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RU200 / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER 0.00015" / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 6061 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.74 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.2 / % possible all: 58.8 |
Reflection | *PLUS Num. obs: 7662 / Num. measured all: 29561 |
Reflection shell | *PLUS % possible obs: 59 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 5RXN Resolution: 1.5→30 Å / σ(F): 0 / Details: ESD FROM CRUIKSHANK (A): 0.08
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.432 / Rfactor obs: 0.389 |