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Open data
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Basic information
Entry | Database: PDB / ID: 1e2r | ||||||
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Title | CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND | ||||||
![]() | NITRITE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / DENITRIFICATION / ELECTRON TRANSPORT / PERIPLASMIC / CYANIDE | ||||||
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: X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus. Authors: Jafferji, A. / Allen, J.W. / Ferguson, S.J. / Fulop, V. #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. #2: ![]() Title: Haem Ligand-Switching During Catalysis in Crystals of a Nitrogen Cycle Enzyme Authors: Williams, P.A. / Fulop, V. / Garman, E.F. / Saunders, N.F.W. / Ferguson, S.J. / Hajdu, J. #3: ![]() Title: The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesys 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 | ![]() | 254.5 KB | Display | ![]() |
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PDB format | ![]() | 202.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.1 KB | Display | ![]() |
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Full document | ![]() | 731.1 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aofS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.721099, 0.545573, 0.427044), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62603.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: SUBSP. PARACOCCUS PANTOTROPHUS FORMALLY KNOWN AS THIOSPHAERA PANTOTROPHA Source: (natural) ![]() References: UniProt: P72181, nitrite reductase (NO-forming), hydroxylamine reductase |
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-Non-polymers , 5 types, 1351 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/DHE.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DHE.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 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: 18 ℃ / 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: Dec 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.83 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→25 Å / Num. obs: 156509 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.145 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 599187 / Rmerge(I) obs: 0.081 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AOF Resolution: 1.59→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 16.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.62 Å / Total num. of bins used: 20
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.23 |