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Yorodumi- PDB-6fsg: Crystal structure of oxidised Flavodoxin 1 from Bacillus cereus (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fsg | ||||||
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Title | Crystal structure of oxidised Flavodoxin 1 from Bacillus cereus (1.27 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 / molecular replacement / Resolution: 1.27 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 | 6fsg.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fsg.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 6fsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fsg_validation.pdf.gz | 788.8 KB | Display | wwPDB validaton report |
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Full document | 6fsg_full_validation.pdf.gz | 791.8 KB | Display | |
Data in XML | 6fsg_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 6fsg_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/6fsg ftp://data.pdbj.org/pub/pdb/validation_reports/fs/6fsg | HTTPS FTP |
-Related structure data
Related structure data | 6fsiC 6ft1C 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 on special symmetry positions |
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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 (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria) Gene: BC_1376 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81G35 |
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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: 2.25 Å3/Da / Density % sol: 45.26 % |
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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: 0.6983 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6983 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→35.2 Å / Num. obs: 38867 / % possible obs: 99.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Rrim(I) all: 0.055 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 9.8 / Num. unique obs: 1722 / CC1/2: 0.992 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / % possible all: 90.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WSB Resolution: 1.27→35.195 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.76 Å2 / Biso mean: 9.6792 Å2 / Biso min: 2.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.27→35.195 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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