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- PDB-2ux1: Identification of two zinc-binding sites in the Streptococcus sui... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ux1 | ||||||
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Title | Identification of two zinc-binding sites in the Streptococcus suis Dpr protein | ||||||
![]() | DNA PROTECTION DURING STARVATION PROTEIN | ||||||
![]() | OXIDOREDUCTASE / METAL-BINDING | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Havukainen, H. / Kauko, A. / Pulliainen, A.T. / Haataja, S. / Meyer-Klaucke, W. / Finne, J. / Papageorgiou, A.C. | ||||||
![]() | ![]() 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 | ![]() | 390.3 KB | Display | ![]() |
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PDB format | ![]() | 320.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 532.9 KB | Display | ![]() |
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Full document | ![]() | 547.9 KB | Display | |
Data in XML | ![]() | 76.9 KB | Display | |
Data in CIF | ![]() | 109.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v15C ![]() 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: 18569.938 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-TERMINUS TRUNCATED. FIRST SEVEN RESIDUES REMOVED. Q8G MUTATION Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9F5J9, UniProt: P0CB53*PLUS, Oxidoreductases; Oxidizing metal ions |
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-Non-polymers , 5 types, 1217 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EPE / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 8 TO GLY ENGINEERED ...ENGINEERED |
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Sequence details | UNIPROT ENTRY HAS FULL LENGTH PROTEIN. PROTEIN DESCRIBED IN THIS PDB-ENTRY HAS TRUNCATED N-TERMINUS ...UNIPROT ENTRY HAS FULL LENGTH PROTEIN. PROTEIN DESCRIBED IN THIS PDB-ENTRY HAS TRUNCATED N-TERMINUS WITH FIRST 7 RESIDUES MISSING AND Q8G MUTATION. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.28 % / Description: NONE |
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Crystal grow | pH: 7.3 Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 400, 0.2 M CACL2, 0.1 M HEPES-NA, PH 7.4 AND 1 MM ZNCL2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 2, 2005 / 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: 1.8→19.97 Å / Num. obs: 180247 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.004 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.98 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.78 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UMN Resolution: 1.8→19.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.651 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / 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: 31.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.97 Å
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Refine LS restraints |
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