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Yorodumi- PDB-8snz: X-ray Crystal Structure of FMN-bound long-chain flavodoxin from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8snz | ||||||
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Title | X-ray Crystal Structure of FMN-bound long-chain flavodoxin from Rhodopseudomonas palustris | ||||||
Components | Flavodoxin | ||||||
Keywords | FLAVOPROTEIN / FMN-bound long chain Flavodoxin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Ansari, A. / Khan, S.A. / Miller, A.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Structure, dynamics, and redox reactivity of an all-purpose flavodoxin. Authors: Khan, S. / Ansari, A. / Brachi, M. / Das, D. / El Housseini, W. / Minteer, S. / Miller, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8snz.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8snz.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 8snz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8snz_validation.pdf.gz | 1012.2 KB | Display | wwPDB validaton report |
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Full document | 8snz_full_validation.pdf.gz | 1013.9 KB | Display | |
Data in XML | 8snz_validation.xml.gz | 15 KB | Display | |
Data in CIF | 8snz_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/8snz ftp://data.pdbj.org/pub/pdb/validation_reports/sn/8snz | HTTPS FTP |
-Related structure data
Related structure data | 8v2yC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17884.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: RPA2117 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N7Y7 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.3-0.6M magnesium formate, 15-20% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 3, 2022 / Details: Osmic VariMax optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→29.35 Å / Num. obs: 16973 / % possible obs: 99.81 % / Redundancy: 7.7 % / Biso Wilson estimate: 30.86 Å2 / CC1/2: 0.983 / Net I/σ(I): 22.71 |
Reflection shell | Resolution: 2.17→2.248 Å / Num. unique obs: 1672 / CC1/2: 0.932 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→29.35 Å / SU ML: 0.292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9867 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→29.35 Å
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Refine LS restraints |
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LS refinement shell |
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