+Open data
-Basic information
Entry | Database: PDB / ID: 3n2s | ||||||
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Title | Structure of NfrA1 nitroreductase from B. subtilis | ||||||
Components | NADPH-dependent nitro/flavin reductase | ||||||
Keywords | OXIDOREDUCTASE / alpga-beta-alpha sandwich | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Morera, S. / Gueguen-Chaignon, V. / Meyer, P. / Cortial, S. / Ouazzani, J. | ||||||
Citation | Journal: Febs Lett. / Year: 2010 Title: NADH oxidase activity of Bacillus subtilis nitroreductase NfrA1: insight into its biological role. Authors: Cortial, S. / Chaignon, P. / Iorga, B.I. / Aymerich, S. / Truan, G. / Gueguen-Chaignon, V. / Meyer, P. / Morera, S. / Ouazzani, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n2s.cif.gz | 210.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n2s.ent.gz | 178.4 KB | Display | PDB format |
PDBx/mmJSON format | 3n2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n2s_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3n2s_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3n2s_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 3n2s_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/3n2s ftp://data.pdbj.org/pub/pdb/validation_reports/n2/3n2s | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28683.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: Bacillus CNCM I-1915 / Gene: nfrA1, nfrA, ywcG, BSU38110, ipa-43d / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P39605, EC: 1.5.1.29 #2: Chemical | ChemComp-FMN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.06 Å3/Da / Density % sol: 40.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG 4000, 200mM sodium acetate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2006 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 64071 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 9.9 / Num. unique all: 8391 / Rsym value: 0.119 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→19.42 Å / Cor.coef. Fo:Fc: 0.9361 / Cor.coef. Fo:Fc free: 0.9248 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.192 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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