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Open data
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Basic information
Entry | Database: PDB / ID: 2v15 | ||||||
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Title | Terbium binding in Streptococcus suis Dpr protein | ||||||
![]() | DNA PROTECTION DURING STARVATION PROTEIN | ||||||
![]() | OXIDOREDUCTASE / IRON / DPS-FAMILY / FERROXIDASE / IRON-BINDING / PEROXIDE RESISTANCE / IRON STORAGE / METAL-BINDING / FERRITIN-LIKE | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Havukainen, H. / Papageorgiou, A.C. / Kauko, A. | ||||||
![]() | ![]() Title: Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins. Authors: Havukainen, H. / Haataja, S. / Kauko, A. / Pulliainen, A.T. / Salminen, A. / Haikarainen, T. / Finne, J. / Papageorgiou, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 373.6 KB | Display | ![]() |
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PDB format | ![]() | 306.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 539.7 KB | Display | ![]() |
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Full document | ![]() | 565 KB | Display | |
Data in XML | ![]() | 70.9 KB | Display | |
Data in CIF | ![]() | 98 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ux1C ![]() 1umnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 18641.014 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172 Source method: isolated from a genetically manipulated source Details: N-TERMINUS TRUNCATED AND FIRST SEVEN RESIDUES REMOVED Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4A3W3, UniProt: P0CB53*PLUS, Oxidoreductases; Oxidizing metal ions |
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-Non-polymers , 5 types, 649 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/TB.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TB.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-TB / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-EPE / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.47 % / Description: NONE |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 2UL AND 2UL VOLUME DROP, 30 % PEG 400, 0.2 M CACL2, 0.1 M HEPES-NAOH, PH 7.4, HANGING DROP,16C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 19, 2004 / Details: MIRRORS |
Radiation | Monochromator: TRIANGULAR HORIZONTAL- FOCUSING SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06276 Å / Relative weight: 1 |
Reflection | Resolution: 2→28 Å / Num. obs: 115331 / % possible obs: 95.6 % / Observed criterion σ(I): 4.57 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Highest resolution: 2.1 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UMN Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.312 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.194 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.98 Å
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Refine LS restraints |
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