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- PDB-3lgq: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lgq | ||||||
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Title | Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite (modified Tyr-303) | ||||||
![]() | Eight-heme nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / alpha protein / eight hemes c | ||||||
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. / Filimonenkov, A.A. / Tikhonova, T.V. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O. | ||||||
![]() | ![]() Title: Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Authors: Trofimov, A.A. / Polyakov, K.M. / Tikhonova, T.V. / Tikhonov, A.V. / Safonova, T.N. / Boyko, K.M. / Dorovatovskii, P.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 | ![]() | 269.2 KB | Display | ![]() |
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PDB format | ![]() | 217 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.8 MB | Display | ![]() |
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Full document | ![]() | 5.8 MB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 80.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lg1C ![]() 3rkhC ![]() 3sceC ![]() 3uu9C ![]() 3gm6S 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: 59491.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ALEN 2 / References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS |
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-Non-polymers , 6 types, 1167 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-SO3 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.36 Å3/Da / Density % sol: 71.54 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution (2.5mcl): 10mg/ml TvNiR, 0.05M Tris hydrochloride (pH7.2). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4- ...Details: Protein solution (2.5mcl): 10mg/ml TvNiR, 0.05M Tris hydrochloride (pH7.2). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol, 0.1M sodium sulfite (pH6.5), 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 30, 2009 |
Radiation | Monochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.8 Å / Num. all: 228946 / Num. obs: 221170 / % possible obs: 96.6 % / Redundancy: 3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / Num. unique all: 17909 / % possible all: 73.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GM6 Resolution: 1.8→19.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.435 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.163 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.167 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.806→1.853 Å / Total num. of bins used: 20
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