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Yorodumi- PDB-4pw3: Crystal structure of the sulfite dehydrogenase SorT from Sinorhiz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pw3 | ||||||
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Title | Crystal structure of the sulfite dehydrogenase SorT from Sinorhizobium meliloti | ||||||
Components | Putative sulfite oxidase | ||||||
Keywords | OXIDOREDUCTASE / SULFITE OXIDASE / SULFITE DEHYDROGENASE / MOLYBDOPTERIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | McGrath, A.P. / Maher, M.J. | ||||||
Citation | Journal: Elife / Year: 2015 Title: Structural basis of interprotein electron transfer in bacterial sulfite oxidation. Authors: McGrath, A.P. / Laming, E.L. / Casas Garcia, G.P. / Kvansakul, M. / Guss, J.M. / Trewhella, J. / Calmes, B. / Bernhardt, P.V. / Hanson, G.R. / Kappler, U. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pw3.cif.gz | 285.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pw3.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/4pw3 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/4pw3 | HTTPS FTP |
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-Related structure data
Related structure data | 4pw9C 4pwaC 2bpbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 39552.684 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 32-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02832, SMc04049 / Plasmid: PPROEXSMC4049 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: Q92M24, sulfite oxidase #2: Chemical | ChemComp-MSS / ( #3: Chemical | #4: 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: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES PH 7.5, 8% ETHYLENE GLYCOL, 0.1M MANGANESE (II) CHLORIDE TETRAHYDRATE, 17.5% PEG 10000 , VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 / Wavelength: 0.95 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2011 | |||||||||||||||
Radiation | Monochromator: SI VORTEX ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.35→50 Å / Num. obs: 77971 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 5.7 | |||||||||||||||
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.669 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2BPB Resolution: 2.35→47.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.881 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→47.64 Å
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Refine LS restraints |
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