+Open data
-Basic information
Entry | Database: PDB / ID: 1y5l | |||||||||
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Title | The crystal structure of the NarGHI mutant NarI-H66Y | |||||||||
Components | (Respiratory nitrate reductase 1 ...) x 3 | |||||||||
Keywords | OXIDOREDUCTASE / nitrate reduction / membrane protein / electron transfer / Q-site | |||||||||
Function / homology | Function and homology information nitrate reductase (quinone) / NarGHI complex / nitrate reductase complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / nitrate assimilation ...nitrate reductase (quinone) / NarGHI complex / nitrate reductase complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Bertero, M.G. / Rothery, R.A. / Boroumand, N. / Palak, M. / Blasco, F. / Ginet, N. / Weiner, J.H. / Strynadka, N.C.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A Authors: Bertero, M.G. / Rothery, R.A. / Boroumand, N. / Palak, M. / Blasco, F. / Ginet, N. / 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 | 1y5l.cif.gz | 421.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y5l.ent.gz | 330.3 KB | Display | PDB format |
PDBx/mmJSON format | 1y5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/1y5l ftp://data.pdbj.org/pub/pdb/validation_reports/y5/1y5l | HTTPS FTP |
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-Related structure data
Related structure data | 1y4zC 1y5iC 1y5nC 1q16S S: Starting model for refinement C: citing same article (ref.) |
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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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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 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) / Strain (production host): LCB79 / 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) / Strain (production host): LCB79 / References: UniProt: P11349, nitrate reductase |
#3: Protein | Mass: 25577.383 Da / Num. of mol.: 1 / Mutation: H66Y 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) / Strain (production host): LCB79 / References: UniProt: P11350, nitrate reductase |
-Non-polymers , 7 types, 361 molecules
#4: Chemical | #5: Chemical | ChemComp-6MO / | #6: Chemical | ChemComp-SF4 / #7: Chemical | ChemComp-3PH / | #8: Chemical | ChemComp-F3S / | #9: Chemical | ChemComp-HEM / | #10: 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: 3.26 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: peg 3000, 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: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2004 / Details: KOHZU: Double Crystal Si(111) |
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: 2.5→25 Å / Num. all: 90666 / Num. obs: 90666 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.111 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Rsym value: 0.482 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q16 Resolution: 2.5→24.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4939977.78 / 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: 18.7808 Å2 / ksol: 0.310009 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→24.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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