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- PDB-3owm: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3owm | ||||||
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Title | Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with hydroxylamine | ||||||
![]() | Eight-heme nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / alpha protein / eight hemes c / Tyr-Cys bond | ||||||
Function / homology | ![]() ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / calcium ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O. | ||||||
![]() | ![]() Title: Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase Authors: Trofimov, A.A. / Polyakov, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.9 KB | Display | ![]() |
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PDB format | ![]() | 222.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.3 MB | Display | ![]() |
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Full document | ![]() | 7.2 MB | Display | |
Data in XML | ![]() | 55.8 KB | Display | |
Data in CIF | ![]() | 83.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f29C ![]() 2ot4S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58834.641 Da / Num. of mol.: 2 / Fragment: UNP residues 33-551 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ALEN 2 / References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS |
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-Non-polymers , 8 types, 1289 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | ChemComp-PG6 / #7: Chemical | ChemComp-PG4 / #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.61 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Protein solution (5mcl): 14.5mg/ml TvNiR, 0.05M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystal ...Details: Protein solution (5mcl): 14.5mg/ml TvNiR, 0.05M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystal was soaked in 0.1M hydroxylamine solution for 30min., VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→12 Å / Num. all: 282622 / Num. obs: 281694 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.65→1.67 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OT4 Resolution: 1.65→12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.891 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.802 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.149 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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