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Yorodumi- PDB-3uu9: Structure of the free TvNiRb form of Thioalkalivibrio nitratiredu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uu9 | ||||||
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Title | Structure of the free TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase | ||||||
Components | Eight-heme nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / Tyr-Cys (CE2-S) bond / Tyr-Gln (CE1-CG) bond | ||||||
Function / homology | Function and homology information 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 | Thioalkalivibrio nitratireducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Trofimov, A.A. / Polyakov, K.M. / Tikhonova, T.V. / Tikhonov, A.V. / Dorovatovskii, P.V. / Popov, V.O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uu9.cif.gz | 264.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uu9.ent.gz | 213.1 KB | Display | PDB format |
PDBx/mmJSON format | 3uu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uu9_validation.pdf.gz | 6.9 MB | Display | wwPDB validaton report |
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Full document | 3uu9_full_validation.pdf.gz | 7 MB | Display | |
Data in XML | 3uu9_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 3uu9_validation.cif.gz | 76.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/3uu9 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/3uu9 | HTTPS FTP |
-Related structure data
Related structure data | 3lg1C 3lgqSC 3rkhC 3sceC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 58921.723 Da / Num. of mol.: 2 / Fragment: UNP residues 33-552 / Source method: isolated from a natural source Source: (natural) Thioalkalivibrio nitratireducens (bacteria) Strain: ALEN 2 References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS, Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor |
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-Non-polymers , 5 types, 935 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PG4 / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.96 Å3/Da / Density % sol: 75.19 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 2.5 uL protein solution (11.6 mg/mL TvNiR in 0.02 M sodium tetraborate, 0.05 M Tris-HCl, pH 8.0) + 2.5 uL reservoir solution (0.2 M trisodium citrate, 0.1 M Tris-HCl, pH 8.5, 30% v/v PEG400, ...Details: 2.5 uL protein solution (11.6 mg/mL TvNiR in 0.02 M sodium tetraborate, 0.05 M Tris-HCl, pH 8.0) + 2.5 uL reservoir solution (0.2 M trisodium citrate, 0.1 M Tris-HCl, pH 8.5, 30% v/v PEG400, 0.1 M hydroxylamine), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.978 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→135.331 Å / Num. all: 117913 / Num. obs: 117676 / % possible obs: 99.8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.2→2.5 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.8 / Num. unique all: 37149 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LGQ Resolution: 2.2→100 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.202 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.124 / 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: 34.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.214 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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