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Yorodumi- PDB-3ak9: Crystal structure of the SEp22 dodecamer, a Dps-like protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ak9 | ||||||
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Title | Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis, FE-soaked form | ||||||
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: 1.3 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 | 3ak9.cif.gz | 769.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ak9.ent.gz | 637.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ak9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3ak9 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3ak9 | HTTPS FTP |
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-Related structure data
Related structure data | 3ak8SC 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
#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-FE2 / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: 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: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: Reservoir solution: 0.1M sodium acetate, 0.3M magnesium chloride, 28% PEG 400. The crystal was soaked in the solution containing 0.1M MES pH6.0, 0.25M magnesium chloride, 30% PEG 400, 0.1M ...Details: Reservoir solution: 0.1M sodium acetate, 0.3M magnesium chloride, 28% PEG 400. The crystal was soaked in the solution containing 0.1M MES pH6.0, 0.25M magnesium chloride, 30% PEG 400, 0.1M ascorbic acid, and 0.1M ferrous ammonium sulfate., 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: 1.3→48.6 Å / Num. all: 448407 / Num. obs: 407378 / % possible obs: 90.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.4 / Num. unique all: 31051 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AK8 Resolution: 1.3→48.6 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.455 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.047 / 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: 25.381 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→48.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.299→1.333 Å / Total num. of bins used: 20
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