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Yorodumi- PDB-6ft1: Crystal structure of oxidised Flavodoxin 1 from Bacillus cereus (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ft1 | ||||||
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Title | Crystal structure of oxidised Flavodoxin 1 from Bacillus cereus (1.4 A resolution) | ||||||
Components | Flavodoxin | ||||||
Keywords | ELECTRON TRANSPORT / flavodoxin / electron transfer / FMN | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Gudim, I. / Lofstad, M. / Hersleth, H.-P. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Protein Sci. / Year: 2018 Title: High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus. Authors: Gudim, I. / Lofstad, M. / van Beek, W. / Hersleth, H.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ft1.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ft1.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ft1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ft1_validation.pdf.gz | 792.7 KB | Display | wwPDB validaton report |
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Full document | 6ft1_full_validation.pdf.gz | 793.7 KB | Display | |
Data in XML | 6ft1_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 6ft1_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/6ft1 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/6ft1 | HTTPS FTP |
-Related structure data
Related structure data | 6fsgC 6fsiC 1wsbS 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: 16115.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: ICO_01211 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R8KEI7, UniProt: Q81G35*PLUS |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-SO4 / |
#4: Sugar | ChemComp-GLC / |
#5: 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: 2.2 Å3/Da / Density % sol: 44.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 3.6 M ammonium sulfate and 0.1 M citric acid pH 4 (final pH 5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.70024 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.70024 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39.291 Å / Num. obs: 28302 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.039 / Rrim(I) all: 0.077 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1382 / CC1/2: 0.671 / Rpim(I) all: 0.293 / Rrim(I) all: 0.524 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WSB Resolution: 1.4→39.291 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.56 Å2 / Biso mean: 14.5425 Å2 / Biso min: 5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→39.291 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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