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Open data
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Basic information
Entry | Database: PDB / ID: 3f4s | ||||||
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Title | Crystal structure of Wolbachia pipientis alpha-DsbA1 T172V | ||||||
![]() | Putative uncharacterized protein | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kurz, M. / Heras, B. / Martin, J.L. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of the Oxidoreductase alpha-DsbA1 from Wolbachia pipientis Authors: Kurz, M. / Iturbe-Ormaetxe, I. / Jarrott, R. / Shouldice, S.R. / Wouters, M.A. / Frei, P. / Glockshuber, R. / O'Neill, S.L. / Heras, B. / Martin, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3f4rSC ![]() 3f4tC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26556.721 Da / Num. of mol.: 1 / Mutation: T172V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PGE / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 22% PEG 3350, 0.1M Ammonium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 5.5-5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 7, 2006 |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→66.33 Å / Num. obs: 31734 / % possible obs: 94.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.6 / % possible all: 62 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3F4R Resolution: 1.55→66.216 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.888 / SU ML: 0.17 / Isotropic thermal model: isotropic and TLS / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 18.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.991 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.97 Å2 / Biso mean: 29.868 Å2 / Biso min: 12.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→66.216 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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