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Yorodumi- PDB-3sxq: Structure of a hexameric multiheme c nitrite reductase from the e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sxq | ||||||
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Title | Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio paradoxus | ||||||
Components | Eight-heme nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / eight hemes c / nitrite reductase | ||||||
Function / homology | Function and homology information nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Thioalkalivibrio paradoxus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Polyakov, K.M. / Trofimov, A.A. / Tikhonova, T.V. / Tikhonov, A.V. / Boyko, K.M. / Popov, V.O. | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species. Authors: Tikhonova, T. / Tikhonov, A. / Trofimov, A. / Polyakov, K. / Boyko, K. / Cherkashin, E. / Rakitina, T. / Sorokin, D. / Popov, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sxq.cif.gz | 273.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sxq.ent.gz | 219 KB | Display | PDB format |
PDBx/mmJSON format | 3sxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sxq_validation.pdf.gz | 5.9 MB | Display | wwPDB validaton report |
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Full document | 3sxq_full_validation.pdf.gz | 6 MB | Display | |
Data in XML | 3sxq_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 3sxq_validation.cif.gz | 82.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sxq ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sxq | HTTPS FTP |
-Related structure data
Related structure data | 3ttbC 2ot4S 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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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: 59228.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thioalkalivibrio paradoxus (bacteria) / Strain: ARh1 / References: UniProt: E7EDQ7 |
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-Non-polymers , 8 types, 1322 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | ChemComp-CO / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-GOL / #9: 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: 5.11 Å3/Da / Density % sol: 75.92 % |
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Crystal grow | Temperature: 278 K / Method: free-interface-diffusion technique / pH: 6.5 Details: 14 mg/mL protein, 0.02M cobalt chloride, 0.1M MES (pH 6.5), 2.8 M ammonium sulfate, free-interface-diffusion technique, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.9 Å / Num. all: 188857 / Num. obs: 186813 / % possible obs: 98.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.47 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.24 / Num. unique all: 26633 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OT4 Resolution: 1.9→29.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.503 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / 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: 15.556 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.147 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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