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Yorodumi- PDB-2bk6: The X-ray crystal structure of the Listeria innocua H31G Dps mutant. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bk6 | ||||||
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Title | The X-ray crystal structure of the Listeria innocua H31G Dps mutant. | ||||||
Components | NON-HEME IRON-CONTAINING FERRITIN | ||||||
Keywords | IRON OXIDATION AND STORAGE / DPS (DNA BINDING PROTEIN FROM STARVED CELLS) / FERROXIDASE CENTER / MUTAGENESIS STUDY / METAL TRANSPORT | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | LISTERIA INNOCUA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Ilari, A. / Latella, M.C. / Ribacchi, F. / Su, M. / Giangiacomo, L. / Stefanini, S. / Chasteen, N.D. / Chiancone, E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants. Authors: Ilari, A. / Latella, M.C. / Ceci, P. / Ribacchi, F. / Su, M. / Giangiacomo, L. / Stefanini, S. / Chasteen, N.D. / Chiancone, E. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron-Binding Site Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bk6.cif.gz | 196 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bk6.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bk6_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 2bk6_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 2bk6_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 2bk6_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bk6 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bk6 | HTTPS FTP |
-Related structure data
Related structure data | 2bjyC 2bkcC 1qghS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 3 / Auth seq-ID: 7 - 156 / Label seq-ID: 7 - 156
NCS oper:
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-Components
#1: Protein | Mass: 17989.459 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Details: H31G MUTANT OF DPS FROM LISTERIA INNOCUA / Source: (gene. exp.) LISTERIA INNOCUA (bacteria) / Plasmid: PET-11A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P80725 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Details: PEG 1000 15-30 % W/V, ACETATE BUFFERS IN A PH RANGE BETWEEN 5.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 57503 / % possible obs: 97.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QGH Resolution: 2.19→119.52 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.576 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.197 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→119.52 Å
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Refine LS restraints |
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