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Yorodumi- PDB-3tdg: Structural and functional characterization of Helicobacter pylori DsbG -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tdg | ||||||
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Title | Structural and functional characterization of Helicobacter pylori DsbG | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / Thioredoxin fold / Reductase | ||||||
Function / homology | Function and homology information Nuclear Transport Factor 2; Chain: A, - #520 / Disulfide isomerase DsbG, N-terminal / Disulfide isomerase DsbG N-terminal / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Yoon, J.Y. / Kim, J. / Lee, S.J. / Kim, H.S. / Im, H.N. / Yoon, H. / Kim, K.H. / Kim, S. / Han, B.W. / Suh, S.W. | ||||||
Citation | Journal: Febs Lett. / Year: 2011 Title: Structural and functional characterization of Helicobacter pylori DsbG Authors: Yoon, J.Y. / Kim, J. / Lee, S.J. / Kim, H.S. / Im, H.N. / Yoon, H. / Kim, K.H. / Kim, S. / Han, B.W. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tdg.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tdg.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tdg_validation.pdf.gz | 709.3 KB | Display | wwPDB validaton report |
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Full document | 3tdg_full_validation.pdf.gz | 712.2 KB | Display | |
Data in XML | 3tdg_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3tdg_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/3tdg ftp://data.pdbj.org/pub/pdb/validation_reports/td/3tdg | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 30571.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_0231 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O25017 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-FMT / |
#4: Chemical | ChemComp-P6G / |
#5: 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: 3.04 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% tacsimate, 28% (w/v) PEG MME 2000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 22035 / % possible obs: 99.4 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.474 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.552 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 48.414 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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