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Open data
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Basic information
Entry | Database: PDB / ID: 1y5i | |||||||||
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Title | The crystal structure of the NarGHI mutant NarI-K86A | |||||||||
![]() | (Respiratory nitrate reductase 1 ...) x 3 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bertero, M.G. / Rothery, R.A. / Boroumand, N. / Palak, M. / Blasco, F. / Ginet, N. / Weiner, J.H. / Strynadka, N.C.J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 445.9 KB | Display | ![]() |
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PDB format | ![]() | 347 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1y4zC ![]() 1y5lC ![]() 1y5nC ![]() 1q16S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 25494.252 Da / Num. of mol.: 1 / Mutation: K86A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 8 types, 1130 molecules ![](data/chem/img/MD1.gif)
![](data/chem/img/6MO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/3PH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AGA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6MO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/3PH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AGA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-6MO / | #6: Chemical | ChemComp-SF4 / ![]() #7: Chemical | ChemComp-F3S / | ![]() #8: Chemical | ChemComp-3PH / | ![]() #9: Chemical | ![]() #10: Chemical | ChemComp-AGA / ( | #11: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 28, 2003 / 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![]() |
Reflection | Resolution: 1.9→30 Å / Num. all: 195380 / Num. obs: 195380 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.424 / % possible all: 76.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1Q16 Resolution: 1.9→29.74 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5731731.12 / 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: 46.7641 Å2 / ksol: 0.347425 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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