+Open data
-Basic information
Entry | Database: PDB / ID: 2c41 | ||||||
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Title | X-ray structure of Dps from Thermosynechococcus elongatus | ||||||
Components | DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN | ||||||
Keywords | IRON-BINDING/OXIDATION PROTEIN / DPS (DNA-BINDING PROTEINS FROM STARVED CELLS) / IRON BINDING / THERMOSTABLE PROTEIN / THERMOPHILIC CYANOBACTERIUM / DNA- BINDING PROTEIN / STRESS PROTEIN / IRON-BINDING-OXIDATION PROTEIN complex | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / DNA binding Similarity search - Function | ||||||
Biological species | THERMOSYNECHOCOCCUS ELONGATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Ilari, A. / Franceschini, S. / Ceci, P. / Chiancone, E. | ||||||
Citation | Journal: FEBS J. / Year: 2006 Title: Antioxidant Dps Protein from the Thermophilic Cyanobacterium Thermosynechococcus Elongatus. Authors: Franceschini, S. / Ceci, P. / Alaleona, F. / Chiancone, E. / Ilari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c41.cif.gz | 392.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c41.ent.gz | 324.9 KB | Display | PDB format |
PDBx/mmJSON format | 2c41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c41_validation.pdf.gz | 538.5 KB | Display | wwPDB validaton report |
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Full document | 2c41_full_validation.pdf.gz | 564.7 KB | Display | |
Data in XML | 2c41_validation.xml.gz | 81.3 KB | Display | |
Data in CIF | 2c41_validation.cif.gz | 115.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c41 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c41 | HTTPS FTP |
-Related structure data
Related structure data | 1ji4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 10 - 158 / Label seq-ID: 10 - 158
NCS oper:
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-Components
#1: Protein | Mass: 17904.373 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Strain: BP-1 / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DG54 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-PGE / #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: 2.08 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | pH: 5 Details: 0.1 M SODIUM ACETATE AT PH VALUES 4.0 AND 5.0, PEG4000 5-15 % |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 174107 / % possible obs: 97.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.7 % / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JI4 Resolution: 1.81→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.212 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.115 / 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: 17.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→30 Å
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Refine LS restraints |
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