+Open data
-Basic information
Entry | Database: PDB / ID: 1siw | ||||||
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Title | Crystal structure of the apomolybdo-NarGHI | ||||||
Components | (Respiratory nitrate reductase 1 ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / apomolybdo-NarGHI / electron-transfer / membrane protein | ||||||
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 / CNS refinement / Resolution: 2.2 Å | ||||||
Authors | Rothery, R.A. / Bertero, M.G. / Cammack, R. / Palak, M. / Blasco, F. / Strynadka, N.C. / Weiner, J.H. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state Authors: Rothery, R.A. / Bertero, M.G. / Cammack, R. / Palak, M. / Blasco, F. / Strynadka, N.C. / Weiner, J.H. #1: Journal: Nat.Struct.Mol.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 | 1siw.cif.gz | 421.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1siw.ent.gz | 337 KB | Display | PDB format |
PDBx/mmJSON format | 1siw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1siw ftp://data.pdbj.org/pub/pdb/validation_reports/si/1siw | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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
-Respiratory nitrate reductase 1 ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 140526.781 Da / Num. of mol.: 1 / Fragment: NarG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Operon narGHJI: NARG, NARC, BISD, B1224 / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P09152, nitrate reductase |
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#2: Protein | Mass: 58140.312 Da / Num. of mol.: 1 / Fragment: NarH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Operon narGHJI: NARH, B1225 / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P11349, nitrate reductase |
#3: Protein | Mass: 25552.355 Da / Num. of mol.: 1 / Fragment: NarI Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Operon narGHJI: NARI, CHLI, B1227 / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P11350, nitrate reductase |
-Non-polymers , 6 types, 608 molecules
#4: Chemical | ChemComp-GDP / | ||||||||
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#5: Chemical | ChemComp-SF4 / #6: Chemical | #7: Chemical | ChemComp-F3S / | #8: Chemical | #9: 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: 2.84 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: peg 3000, hepes, sodium acetate, potassium chloride, edta, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 28, 2003 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 131933 / Num. obs: 128499 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.084 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.351 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: CNS refinement / Resolution: 2.2→29.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5806555.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4484 Å2 / ksol: 0.324775 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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