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Open data
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Basic information
Entry | Database: PDB / ID: 4xs6 | ||||||
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Title | Salmonella typhimurium AhpC W81F mutant | ||||||
![]() | Alkyl hydroperoxide reductase subunit C | ||||||
![]() | OXIDOREDUCTASE / peroxiredoxin / LU / PrxI / conformation | ||||||
Function / homology | ![]() NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / cellular response to stress / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perkins, A. / Nelson, K. / Parsonage, D. / Poole, L. / Karplus, P.A. | ||||||
![]() | ![]() Title: Experimentally Dissecting the Origins of Peroxiredoxin Catalysis. Authors: Nelson, K.J. / Perkins, A. / Van Swearingen, A.E.D. / Hartman, S. / Brereton, A.E. / Parsonage, D. / Salsbury Jr., F.R. / Karplus, P.A. / Poole, L.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.7 KB | Display | ![]() |
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PDB format | ![]() | 277.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.9 KB | Display | ![]() |
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Full document | ![]() | 511.3 KB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xraC ![]() 4xrdC ![]() 4xs1C ![]() 4xs4C ![]() 4xtsC ![]() 5ukaC ![]() 4ma9S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 20602.152 Da / Num. of mol.: 5 / Mutation: W81F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-K / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.4 M MgSO4, 0.1 M MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→71.9 Å / Num. obs: 21119 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 3.35→3.53 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MA9 Resolution: 3.35→71.889 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 0.29 / Phase error: 29.03 / 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: 3.35→71.889 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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