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- PDB-2cf7: Asp74Ala mutant crystal structure for Dps-like peroxide resistanc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cf7 | ||||||
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Title | Asp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from Streptococcus suis. | ||||||
![]() | DPR | ||||||
![]() | PEROXIDE RESISTANCE / DPS-FAMILY / FERRITIN-LIKE / FERROXIDASE / IRON-BINDING | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kauko, A. / Pulliainen, A.T. / Haataja, S. / Finne, J. / Papageorgiou, A.C. | ||||||
![]() | ![]() Title: Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase center and leads to the formation of a ferrihydrite-like core. Authors: Kauko, A. / Pulliainen, A.T. / Haataja, S. / Meyer-Klaucke, W. / 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 | ![]() | 413.1 KB | Display | ![]() |
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PDB format | ![]() | 343.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 519.6 KB | Display | ![]() |
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Full document | ![]() | 539.6 KB | Display | |
Data in XML | ![]() | 89.3 KB | Display | |
Data in CIF | ![]() | 130.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bw1C ![]() 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 18525.928 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-TERMINUS TRUNCATED AND FIRST SEVEN RESIDUES REMOVED Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EPE / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 74 TO ALA ...ENGINEERED | 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. THIS PROTEIN HAS ALSO D74A MUTATION. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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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 MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8128 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 308623 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 22.91 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UMN Resolution: 1.5→19.28 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.763 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ONE ROUND OF REFINEMENT WITH ALL DATA WAS RUN AFTER THE WORKING AND TEST SETS WERE MERGED.
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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: 17.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.28 Å
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Refine LS restraints |
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