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Yorodumi- PDB-3ak8: Crystal structure of the SEp22 dodecamer, a Dps-like protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ak8 | ||||||
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Title | Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis | ||||||
Components | DNA protection during starvation protein | ||||||
Keywords | METAL BINDING PROTEIN / Oxidoreductase / Dps-like protein / dodecamer / Iron-binding protein | ||||||
Function / homology | Ferritin, core subunit, four-helix bundle / Ferritin / Up-down Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Kentucky (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Miyamoto, T. / Asahina, Y. / Miyazaki, S. / Shimizu, H. / Ohto, U. / Noguchi, S. / Satow, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structures of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis Authors: Miyamoto, T. / Asahina, Y. / Miyazaki, S. / Shimizu, H. / Ohto, U. / Noguchi, S. / Satow, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ak8.cif.gz | 784.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ak8.ent.gz | 651.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ak8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ak8_validation.pdf.gz | 523.6 KB | Display | wwPDB validaton report |
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Full document | 3ak8_full_validation.pdf.gz | 535.3 KB | Display | |
Data in XML | 3ak8_validation.xml.gz | 81 KB | Display | |
Data in CIF | 3ak8_validation.cif.gz | 117.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3ak8 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3ak8 | HTTPS FTP |
-Related structure data
Related structure data | 3ak9C 1dpsS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 18742.254 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Kentucky (bacteria) Strain: CVM29188 / Plasmid: pMAL-p2X / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: B3YEF4, Oxidoreductases; Oxidizing metal ions #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / #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: 2.16 Å3/Da / Density % sol: 43.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 0.1M sodium acetate, 0.3M magnesium chloride, 28% PEG 400, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2009 |
Radiation | Monochromator: TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. all: 532649 / Num. obs: 531051 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.25→1.283 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.43 / Num. unique all: 38022 / % possible all: 97.02 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DPS Resolution: 1.25→36.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.744 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.048 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.959 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→36.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.283 Å / Total num. of bins used: 20
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