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Yorodumi- PDB-3bvk: Structural basis for the iron uptake mechanism of Helicobacter py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bvk | ||||||
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Title | Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin | ||||||
Components | Ferritin | ||||||
Keywords | OXIDOREDUCTASE / iron storage / Metal-binding | ||||||
Function / homology | Function and homology information bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, K.H. / Cho, K.J. / Lee, J.H. / Shin, H.J. / Yang, I.S. | ||||||
Citation | Journal: To be Published Title: Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin Authors: Kim, K.H. / Cho, K.J. / Lee, J.H. / Shin, H.J. / Yang, I.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bvk.cif.gz | 450.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bvk.ent.gz | 369.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bvk_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 3bvk_full_validation.pdf.gz | 500.7 KB | Display | |
Data in XML | 3bvk_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 3bvk_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bvk ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bvk | HTTPS FTP |
-Related 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: 20957.465 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZLI1, ferroxidase #2: Chemical | ChemComp-FE / #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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, 10% isopropanol, 200 mM sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 212629 / Num. obs: 208376 / % possible obs: 98 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.9 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.322 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.067 / 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: 16.681 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→23.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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