+Open data
-Basic information
Entry | Database: PDB / ID: 3f4t | ||||||
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Title | Crystal structure of Wolbachia pipientis alpha-DsbA1 C97A/C146A | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin-fold / DSBA | ||||||
Function / homology | Function and homology information protein-disulfide reductase (glutathione) activity / protein disulfide isomerase activity Similarity search - Function | ||||||
Biological species | Wolbachia pipientis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kurz, M. / Heras, B. / Martin, J.L. | ||||||
Citation | Journal: ANTIOXID.REDOX SIGNAL. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f4t.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f4t.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f4t_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 3f4t_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 3f4t_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3f4t_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/3f4t ftp://data.pdbj.org/pub/pdb/validation_reports/f4/3f4t | HTTPS FTP |
-Related structure data
Related structure data | 3f4rSC 3f4sC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26494.564 Da / Num. of mol.: 1 / Mutation: C97A, C146A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolbachia pipientis (bacteria) / Strain: wMel / Gene: WD_1055 / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q73GA4 |
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#2: Chemical | ChemComp-PGE / |
#3: Chemical | ChemComp-1PE / |
#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: 2.21 Å3/Da / Density % sol: 44.32 % |
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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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 14, 2006 |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40.1 Å / Num. obs: 19850 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.79 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F4R Resolution: 1.85→40.059 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.867 / SU ML: 0.24 / Isotropic thermal model: isotropic and TLS / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 20.36 / 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: 72.374 Å2 / ksol: 0.377 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.68 Å2 / Biso mean: 30.878 Å2 / Biso min: 10.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.059 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: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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