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Open data
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Basic information
Entry | Database: PDB / ID: 2c2f | ||||||
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Title | Dps from Deinococcus radiodurans | ||||||
![]() | DNA-BINDING STRESS RESPONSE PROTEIN | ||||||
![]() | DNA BINDING PROTEIN / DPS / IRON / DEINOCOCCUS RADIODURANS / DNA-BINDING PROTEIN | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Romao, C.V. / Mitchell, E. / McSweeney, S. | ||||||
![]() | ![]() Title: The Crystal Structure of Deinococcus Radiodurans Dps Protein (Dr2263) Reveals the Presence of a Novel Metal Centre in the N Terminus. Authors: Romao, C.V. / Mitchell, E. / Mcsweeney, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55 KB | Display | ![]() |
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PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
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Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23050.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R1 / Plasmid: PDEST14 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 286 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % Description: DATA WERE COLLECTED REMOTE TO THE ANOMALOUS ABSORPTION EDGES OF ZN AND FE. |
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Crystal grow | pH: 8 Details: 200MM LITHIUM SULFATE, 100MM TRIS-HCL PH8.5, 15% PEG4000, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 23, 2004 / Details: MULTI-LAYER MIRROR |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→31.91 Å / Num. obs: 32579 / % possible obs: 100 % / Redundancy: 84 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 56.5 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 84.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 11.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE OCCUPANIES OF ATOMS HAVING OCCUPANCIES LOWER THAN 1 WERE ESTIMATED FROM THEIR ATOMIC B-FACTORS. THE FIRST 29 AMINO ACID RESIDUES WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE OCCUPANIES OF ATOMS HAVING OCCUPANCIES LOWER THAN 1 WERE ESTIMATED FROM THEIR ATOMIC B-FACTORS. THE FIRST 29 AMINO ACID RESIDUES WERE NOT MODELLED BECAUSE IT WAS NOT POSSIBLE TO ALLOCATE THE ELECTRON DENSITY.
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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: 14.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→64.02 Å
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Refine LS restraints |
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