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- PDB-2bw1: Iron-bound crystal structure of Dps-like peroxide resistance prot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bw1 | ||||||
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Title | Iron-bound crystal structure of Dps-like peroxide resistance protein (Dpr) from Streptococcus suis. | ||||||
![]() | DPS-LIKE PEROXIDE RESISTANCE PROTEIN | ||||||
![]() | PEROXIDE RESISTANCE / DPR / IRON-BINDING / FERROXIDASE / DPS-FAMILY / FERRITIN-LIKE | ||||||
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. / 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 | ![]() | 404.2 KB | Display | ![]() |
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PDB format | ![]() | 333.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.9 KB | Display | ![]() |
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Full document | ![]() | 540.1 KB | Display | |
Data in XML | ![]() | 83.6 KB | Display | |
Data in CIF | ![]() | 118.9 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 18569.938 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 | ChemComp-FE / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED MUTATION GLN 8 TO GLY IN CHAINS A-L. ONLY THE CHAIN G MUTATION WAS VISIBLE IN THE ...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. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % Description: A 2.81A DATASET FOR THIS STRUCTURE WAS USED AS STARTING MODEL. |
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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: 0.8128 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 188319 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6 / Rsym value: 0.34 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: STRUCTURE FROM PREVIOUS DATASET Resolution: 1.81→19.53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.178 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: LAST CYCLE OF REFINEMENT WAS DONE WITHOUT R-FREE SET. STATISTICS RELATED TO R-FREE ARE FORM SECOND LAST CYCLE. CRYSTAL SOAKED FOR 10 MIN IN 10 MM (NH4) 2FE(SO4)2 AND 2.5 PERCENT (SO2NA)2 I.E. REDUCTANT.
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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: 24.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→19.53 Å
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Refine LS restraints |
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