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Yorodumi- PDB-2a3p: Structure of Desulfovibrio desulfuricans G20 tetraheme cytochrome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a3p | |||||||||
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Title | Structure of Desulfovibrio desulfuricans G20 tetraheme cytochrome with bound molybdate | |||||||||
Components | COG3005: Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit | |||||||||
Keywords | ELECTRON TRANSPORT / Desulfovibrio / tetraheme cytochrome / cytochrome c3 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Pattarkine, M.V. / Lee, Y.-H. / Tanner, J.J. / Wall, J.D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Desulfovibrio desulfuricans G20 Tetraheme Cytochrome Structure at 1.5A and Cytochrome Interaction with Metal Complexes Authors: Pattarkine, M.V. / Tanner, J.J. / Bottoms, C.A. / Lee, Y.-H. / Wall, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a3p.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a3p.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 2a3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a3p_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2a3p_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2a3p_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2a3p_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/2a3p ftp://data.pdbj.org/pub/pdb/validation_reports/a3/2a3p | HTTPS FTP |
-Related structure data
Related structure data | 2a3mSC 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
#1: Protein | Mass: 14173.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria) Species: Desulfovibrio desulfuricans / Strain: G20 / Species (production host): Desulfovibrio desulfuricans Production host: Desulfovibrio desulfuricans subsp. desulfuricans str. G20 (bacteria) Strain (production host): subsp. desulfuricans str. G20 / References: UniProt: Q30WH0 | ||||
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#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-MOO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 4000, 5% ethylene glycol, 0.2M ZnCl2, 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. obs: 5706 / % possible obs: 96.5 % / Rmerge(I) obs: 0.097 / Χ2: 0.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A3M Resolution: 2.3→27.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.338 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.632 / ESU R Free: 0.278 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.371 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 14.7 Å / Origin y: 0.766 Å / Origin z: 4.6 Å
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Refinement TLS group | Selection: ALL |