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Yorodumi- PDB-2nya: Crystal structure of the periplasmic nitrate reductase (NAP) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nya | ||||||
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Title | Crystal structure of the periplasmic nitrate reductase (NAP) from Escherichia coli | ||||||
Components | Periplasmic nitrate reductase | ||||||
Keywords | OXIDOREDUCTASE / Molybdenum / Nitrate Reductase | ||||||
Function / homology | Function and homology information nitrate reductase complex / nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / anaerobic respiration / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding ...nitrate reductase complex / nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / anaerobic respiration / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jepson, B.J.N. / Richardson, D.J. / Hemmings, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli Authors: Jepson, B.J. / Mohan, S. / Clarke, T.A. / Gates, A.J. / Cole, J.A. / Butler, C.S. / Butt, J.N. / Hemmings, A.M. / Richardson, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nya.cif.gz | 346.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nya.ent.gz | 277.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/2nya ftp://data.pdbj.org/pub/pdb/validation_reports/ny/2nya | HTTPS FTP |
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-Related structure data
Related structure data | 2napS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a monomer. Two copies are found in the asymmetric unit. |
-Components
#1: Protein | Mass: 89618.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: napA / Plasmid: pJG460 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB2048 / References: UniProt: P33937, nitrate reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MGD / #5: 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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4000, 10% 2-propanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] and Ge [220]. Focussed by toroidal Zerodur mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 56862 / Num. obs: 56852 / % possible obs: 97.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 5.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NAP Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.18 / SU ML: 0.243 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.451 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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