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- PDB-4pw3: Crystal structure of the sulfite dehydrogenase SorT from Sinorhiz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pw3 | ||||||
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Title | Crystal structure of the sulfite dehydrogenase SorT from Sinorhizobium meliloti | ||||||
![]() | Putative sulfite oxidase | ||||||
![]() | OXIDOREDUCTASE / SULFITE OXIDASE / SULFITE DEHYDROGENASE / MOLYBDOPTERIN | ||||||
Function / homology | ![]() sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McGrath, A.P. / Maher, M.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.9 KB | Display | ![]() |
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PDB format | ![]() | 229.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 54.6 KB | Display | |
Data in CIF | ![]() | 75.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pw9C ![]() 4pwaC ![]() 2bpbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-MSS / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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