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- PDB-3mmo: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mmo | ||||||
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Title | Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with cyanide | ||||||
![]() | 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. / Tikhonova, T.V. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O. | ||||||
![]() | ![]() Title: Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide. Authors: Trofimov, A.A. / Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Safonova, T.N. / Tikhonov, A.V. / Popov, A.N. / 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 | ![]() | 399.4 KB | Display | ![]() |
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PDB format | ![]() | 328.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fo3C ![]() 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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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 , 8 types, 1265 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/TRS.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-PG4 / #7: Chemical | ChemComp-TRS / | #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: 4.23 Å3/Da / Density % sol: 70.7 % |
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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 KCN for 1h, 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: 1.55→12 Å / Num. all: 350567 / Num. obs: 350257 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.55→1.57 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.9 / Num. unique all: 11650 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OT4 Resolution: 1.55→11.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.769 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045 / 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: 18.046 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.14 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→11.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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