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- PDB-1o9r: The X-ray crystal structure of Agrobacterium tumefaciens Dps, a m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o9r | ||||||
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Title | The X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the family that protect DNA without binding | ||||||
![]() | AGROBACTERIUM TUMEFACIENS DPS | ||||||
![]() | IRON-BINDING PROTEIN / DNA PROTECTION FROM OXIDATIVE DAMAGE / DNA-BINDING / IRON- BINDING PROTEIN | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ilari, A. / Ceci, P. / Chiancone, E. | ||||||
![]() | ![]() Title: The Dps Protein of Agrobacterium Tumefaciens Does not Bind to DNA But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, and Hydroxyl-Radical Scavenging Properties Authors: Ceci, P. / Ilari, A. / Falvo, E. / Chiancone, E. #1: ![]() Title: Structure of the Neutrophil-Activating Protein from Helicobacter Pylori Authors: Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Giudice, G.D. / Rappuoli, R. / Montecucco, C. #2: ![]() Title: Structure of Two Iron-Binding Proteins from Bacillus Anthracis Authors: Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G. #3: ![]() Title: The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron-Binding Site Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D. #4: ![]() Title: The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.2 KB | Display | ![]() |
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PDB format | ![]() | 166.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1dpsS S: Starting model for refinement |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 17847.086 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: HEPES 0.1 M, PH 7.0-7.8, ETHYLENE GLYCOL IN A RANGE BETWEEN 16%-24% V/V | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 179135 / % possible obs: 96 % / Observed criterion σ(I): 0.9 / Redundancy: 5 % / Biso Wilson estimate: 12.44 Å2 / Rmerge(I) obs: 0.053 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 96 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DPS Resolution: 1.45→20 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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