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Open data
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Basic information
Entry | Database: PDB / ID: 1gq1 | ||||||
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Title | CYTOCHROME CD1 NITRITE REDUCTASE, Y25S mutant, OXIDISED FORM | ||||||
![]() | CYTOCHROME CD1 NITRITE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / REDUCTASE / ENZYME / NITRITE REDUCTASE / DENITRIFICATION / ELECTRON TRANSPORT / PERIPLASMIC | ||||||
Function / homology | ![]() hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sjogren, T. / Gordon, E.H.J. / Lofqvist, M. / Richter, C.D. / Hajdu, J. / Ferguson, S.J. | ||||||
![]() | ![]() Title: Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine Authors: Gordon, E.H.J. / Sjogren, T. / Lofqvist, M. / Richter, C.D. / Allen, J. / Higham, C. / Hajdu, J. / Fulop, V. / Ferguson, S.J. #1: ![]() Title: The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesis of Nitric Oxide by Cytochrome Cd1 Authors: Fulop, V. / Moir, J.W.B. / Ferguson, S.J. / Hajdu, 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 | ![]() | 263.6 KB | Display | ![]() |
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PDB format | ![]() | 209.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 56.1 KB | Display | |
Data in CIF | ![]() | 85.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qksS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62470.438 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9FCQ0, UniProt: P72181*PLUS, EC: 1.9.3.2, nitrite reductase (NO-forming) |
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-Non-polymers , 5 types, 1369 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DHE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DHE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 2.3 M AMMONIUM SULFATE, 50MM POTASSIUM PHOSPHATE, PH 7.0, AND CRYOPROTECTANT 18% GLYCEROL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Fulop, V., (1993) J. Mol. Biol., 232, 1211. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 6, 2000 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 233906 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 812906 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 100 % / Mean I/σ(I) obs: 4.72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QKS Resolution: 1.4→30 Å / SU B: 0.79 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.05 / ESU R Free: 0.05
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Displacement parameters | Biso mean: 10.9 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 4 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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