+Open data
-Basic information
Entry | Database: PDB / ID: 5imf | ||||||
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Title | Xanthomonas campestris Peroxiredoxin Q - Structure F5 | ||||||
Components | Bacterioferritin comigratory protein | ||||||
Keywords | OXIDOREDUCTASE / PrxQ / BCP / Peroxidase / redox | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Perkins, A. / Parsonage, D. / Nelson, K.J. / Poole, L.B. / Karplus, A. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Peroxiredoxin Catalysis at Atomic Resolution. Authors: Perkins, A. / Parsonage, D. / Nelson, K.J. / Ogba, O.M. / Cheong, P.H. / Poole, L.B. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5imf.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5imf.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 5imf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/5imf ftp://data.pdbj.org/pub/pdb/validation_reports/im/5imf | HTTPS FTP |
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-Related structure data
Related structure data | 5iizC 5im9C 5imaC 5imcC 5imdC 5imvC 5imzC 5inyC 5io0C 5io2C 5iowC 5ioxC 5ipgC 5iphC 3gkmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17226.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria) Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: XCC1738 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P9V9 | ||||
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#2: Chemical | #3: Chemical | ChemComp-FMT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.43 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 30% PEG 4000, 0.1 M sodium acetate pH 5.5, 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97648 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→23.15 Å / Num. obs: 60776 / % possible obs: 90.5 % / Redundancy: 6.3 % / CC1/2: 0.453 / Net I/σ(I): 11.3 |
Reflection shell | Highest resolution: 1.04 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3gkm Resolution: 1.04→23.15 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 17.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→23.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.04→1.0518 Å
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