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Yorodumi- PDB-3klj: Crystal structure of NADH:rubredoxin oxidoreductase from Clostrid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3klj | ||||||
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Title | Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum | ||||||
Components | NAD(FAD)-dependent dehydrogenase, NirB-family (N-terminal domain) | ||||||
Keywords | OXIDOREDUCTASE / FAD-binding protein / GR-fold | ||||||
Function / homology | Function and homology information rubredoxin-NAD+ reductase / rubredoxin-NAD+ reductase activity / oxygen metabolic process / response to toxic substance / flavin adenine dinucleotide binding / electron transfer activity Similarity search - Function | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nishikawa, K. / Shomura, Y. / Kawasaki, S. / Niimura, Y. / Higuchi, Y. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum: a key component of the dioxygen scavenging system in obligatory anaerobes. Authors: Nishikawa, K. / Shomura, Y. / Kawasaki, S. / Niimura, Y. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3klj.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3klj.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3klj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3klj ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42166.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: nror, CA_C2448 / Plasmid: pET7Blue, pNROR / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q9AL95, rubredoxin-NAD+ reductase |
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#2: Chemical | ChemComp-FAD / |
#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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 35% (v/v) PEG 400, 0.1M Tris-HCl pH 8.5, 0.15M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 25983 / Num. obs: 25983 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4806 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.663 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.958 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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