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Yorodumi- PDB-1q16: Crystal structure of Nitrate Reductase A, NarGHI, from Escherichi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q16 | ||||||
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Title | Crystal structure of Nitrate Reductase A, NarGHI, from Escherichia coli | ||||||
Components | (Respiratory nitrate reductase 1 ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / membrane protein / electron-transfer | ||||||
Function / homology | Function and homology information nitrate reductase (quinone) / nitrate reductase complex / NarGHI complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / molybdopterin cofactor binding / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nitrate assimilation ...nitrate reductase (quinone) / nitrate reductase complex / NarGHI complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / molybdopterin cofactor binding / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å | ||||||
Authors | Bertero, M.G. / Strynadka, N.C.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A Authors: Bertero, M.G. / Rothery, R.A. / Palak, M. / Hou, C. / Lim, D. / Blasco, F. / Weiner, J.H. / Strynadka, N.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q16.cif.gz | 441.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q16.ent.gz | 356.1 KB | Display | PDB format |
PDBx/mmJSON format | 1q16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q16_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1q16_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1q16_validation.xml.gz | 83.2 KB | Display | |
Data in CIF | 1q16_validation.cif.gz | 121 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q16 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q16 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Respiratory nitrate reductase 1 ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 140657.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narG / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / References: UniProt: P09152, nitrate reductase |
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#2: Protein | Mass: 58140.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narH / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / References: UniProt: P11349, nitrate reductase |
#3: Protein | Mass: 25552.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narI / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / References: UniProt: P11350, nitrate reductase |
-Non-polymers , 8 types, 1225 molecules
#4: Chemical | #5: Chemical | ChemComp-6MO / | #6: Chemical | ChemComp-SF4 / #7: Chemical | ChemComp-AGA / ( | #8: Chemical | ChemComp-F3S / | #9: Chemical | ChemComp-3PH / | #10: Chemical | #11: 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: 2.89 Å3/Da / Density % sol: 57.45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3000, sodium acetate, potassium chloride, EDTA, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2002 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 202288 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 10 Å2 / Rsym value: 0.081 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 203816 / % possible obs: 99.6 % / Num. measured all: 1267890 / Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.502 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→29.68 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 7975224.84 / Data cutoff high rms absF: 7975224.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.9332 Å2 / ksol: 0.336417 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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