+Open data
-Basic information
Entry | Database: PDB / ID: 5l89 | |||||||||
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Title | Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A | |||||||||
Components | Rru_A0973 | |||||||||
Keywords | OXIDOREDUCTASE / ferritin / iron oxidation / ferroxidase | |||||||||
Function / homology | Function and homology information encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodospirillum rubrum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | He, D. / Hughes, S. / Vanden-Hehir, S. / Georgiev, A. / Altenbach, K. / Tarrant, E. / Mackay, C.L. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J. | |||||||||
Funding support | China, United Kingdom, 2items
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Citation | Journal: Elife / Year: 2016 Title: Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. Authors: He, D. / Hughes, S. / Vanden-Hehir, S. / Georgiev, A. / Altenbach, K. / Tarrant, E. / Mackay, C.L. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l89.cif.gz | 988.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l89.ent.gz | 833.6 KB | Display | PDB format |
PDBx/mmJSON format | 5l89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l89_validation.pdf.gz | 620.1 KB | Display | wwPDB validaton report |
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Full document | 5l89_full_validation.pdf.gz | 627.5 KB | Display | |
Data in XML | 5l89_validation.xml.gz | 76.2 KB | Display | |
Data in CIF | 5l89_validation.cif.gz | 112.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l89 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l89 | HTTPS FTP |
-Related structure data
Related structure data | 5da5SC 5l8bC 5l8gC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13289.638 Da / Num. of mol.: 30 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: Rru_A0973 / Plasmid: Plasmid / Details (production host): pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2RVS1 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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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: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1-2 ul protein mixed with 1 ul well solution over 1 ml well solution 14% PEG3350 + 0.14 M CaAc PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7311 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015 |
Radiation | Monochromator: Double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7311 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.84 Å / Num. obs: 100067 / % possible obs: 99 % / Redundancy: 4.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.171 / Rsym value: 0.196 / Net I/σ(I): 8.46 |
Reflection shell | Resolution: 2.59→2.683 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.79 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DA5 Resolution: 2.59→48.84 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→48.84 Å
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Refine LS restraints |
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LS refinement shell |
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