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- PDB-4o5r: Crystal structure of Alkylhydroperoxide Reductase subunit C from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4o5r | ||||||
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Title | Crystal structure of Alkylhydroperoxide Reductase subunit C from E. coli | ||||||
![]() | AhpC component, subunit of alkylhydroperoxide reductase | ||||||
![]() | OXIDOREDUCTASE / hydrogen peroxide | ||||||
Function / homology | ![]() NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / cellular response to stress / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dip, P.V. / Kamariah, N. / Manimekalai, M.S.S. / Gruber, G. / Eisenhaber, F. / Eisenhaber, B. | ||||||
![]() | ![]() Title: Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli Authors: Dip, P.V. / Kamariah, N. / Subramanian Manimekalai, M.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G. #1: ![]() Title: Peroxiredoxin Evolution and the Regulation of Hydrogen Peroxide Signaling Authors: Wood, Z.A. / Poole, L.B. / Karplus, P.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.6 KB | Display | ![]() |
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PDB format | ![]() | 271.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.6 KB | Display | ![]() |
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Full document | ![]() | 455 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4o5qC ![]() 4o5uC ![]() 3empS 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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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 5 - 160 / Label seq-ID: 5 - 160
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Details | decamer generated by symmetry operation from the assymetric unit |
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Components
#1: Protein | Mass: 20786.412 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C6EK89, UniProt: A0A140NC97*PLUS, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor, peroxiredoxin |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M ammonium sulfate, 100mM MES, pH 6.5, 5% dioxane , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.33→147.45 Å / Num. obs: 23735 / % possible obs: 99.2 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Rsym value: 0.067 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.33→3.51 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.484 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EMP Resolution: 3.33→29.74 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.826 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 52.831 / SU ML: 0.354 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.519 / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.32 Å2
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Refinement step | Cycle: LAST / Resolution: 3.33→29.74 Å
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Refine LS restraints |
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