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Yorodumi- PDB-8ffc: Crystal structure of iron bound Dps protein (PA0962) from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ffc | |||||||||
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Title | Crystal structure of iron bound Dps protein (PA0962) from Pseudomonas aeruginosa (cubic form) | |||||||||
Components | Probable dna-binding stress protein | |||||||||
Keywords | METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rivera, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity. Authors: Rajapaksha, N. / Soldano, A. / Yao, H. / Donnarumma, F. / Kashipathy, M.M. / Seibold, S. / Battaile, K.P. / Lovell, S. / Rivera, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ffc.cif.gz | 530 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ffc.ent.gz | 439.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ffc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/8ffc ftp://data.pdbj.org/pub/pdb/validation_reports/ff/8ffc | HTTPS FTP |
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-Related structure data
Related structure data | 8ff9C 8ffaC 8ffbC 8ffdC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17510.916 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0962 / Plasmid: PET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9I4Z7 #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-EPE / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8% (w/v) PEG 8000, 100 mM Hepes. Soaking: crystals were transferred to a solution containing 80% crystallant, 20% PEG 200 and 50 mM FeCl2 and soaked for 10 minutes. Samples were harvested ...Details: 8% (w/v) PEG 8000, 100 mM Hepes. Soaking: crystals were transferred to a solution containing 80% crystallant, 20% PEG 200 and 50 mM FeCl2 and soaked for 10 minutes. Samples were harvested directly from the soaking solution |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 7, 2020 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.86 Å / Num. obs: 315151 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.034 / Rrim(I) all: 0.153 / Χ2: 1.01 / Net I/σ(I): 15.2 / Num. measured all: 6542757 |
Reflection shell | Resolution: 1.85→1.88 Å / % possible obs: 100 % / Redundancy: 21 % / Rmerge(I) obs: 1.985 / Num. measured all: 325945 / Num. unique obs: 15535 / CC1/2: 0.684 / Rpim(I) all: 0.444 / Rrim(I) all: 2.035 / Χ2: 0.99 / Net I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→43.91 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 20.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→43.91 Å
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Refine LS restraints |
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LS refinement shell |
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