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Open data
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Basic information
Entry | Database: PDB / ID: 1qks | ||||||
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Title | CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM | ||||||
![]() | CYTOCHROME CD1 NITRITE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / 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 | ![]() ![]() ![]() | ||||||
![]() | Fulop, V. | ||||||
![]() | ![]() 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. / Ferguson, S.J. / Hajdu, J. #1: Journal: J.Mol.Biol. / Year: 1997 Title: Cytochrome Cd1 Structure: Unusual Haem Environments in a Nitrite Reductase and Analysis of Factors Contributing to Beta-Propeller Folds Authors: Baker, S.C. / Saunders, N.F.W. / Willis, A.C. / Ferguson, S.J. / Hajdu, J. / Fulop, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259 KB | Display | ![]() |
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PDB format | ![]() | 216.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.3 KB | Display | ![]() |
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Full document | ![]() | 741.7 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.71269, 0.52853, 0.46124), Vector: Details | MOLECULE IS A HOMO-DIMERIC-COMPLEX. | |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62605.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 1528 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DHE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DHE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: 2.3 M AMMONIUM SULFATE, 50MM POTASSIUM PHOSPHATE, PH 7.0, AND CRYOPROTECTANT 15% GLYCEROL | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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: Mar 15, 1995 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→20 Å / Num. obs: 278611 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.073 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 8 / Rsym value: 0.098 / % possible all: 80.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 13.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.3 Å / Total num. of bins used: 20
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.21 |