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Yorodumi- PDB-1yep: Structural and biochemical analysis of the link between enzymatic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yep | |||||||||
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Title | Structural and biochemical analysis of the link between enzymatic activity and olgomerization in AhpC, a bacterial peroxiredoxin. | |||||||||
Components | Alkyl hydroperoxide reductase subunit C | |||||||||
Keywords | OXIDOREDUCTASE / AHPC / Peroxiredoxin / peroxidase | |||||||||
Function / homology | Function and homology information 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 | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Parsonage, D. / Youngblood, D.S. / Sarma, G.N. / Wood, Z.A. / Karplus, P.A. / Poole, L.B. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Analysis of the Link between Enzymatic Activity and Oligomeric State in AhpC, a Bacterial Peroxiredoxin. Authors: Parsonage, D. / Youngblood, D.S. / Sarma, G.N. / Wood, Z.A. / Karplus, P.A. / Poole, L.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yep.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yep.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1yep ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1yep | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20641.188 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: ahpC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A251, peroxiredoxin #2: Chemical | ChemComp-SO4 / #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: 3.6 Å3/Da / Density % sol: 65.82 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 50360 / Num. obs: 50360 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 92.2 |
-Processing
Software |
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Refinement | Resolution: 2.5→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Waters have been sorted by chain contact and electron density. The water number thousandth place indicates the protein chain it is in contact with (A=1, B=2, etc.) and within each series an ...Details: Waters have been sorted by chain contact and electron density. The water number thousandth place indicates the protein chain it is in contact with (A=1, B=2, etc.) and within each series an increase in number corresponds to a decrease in average peak density of equivalent waters from different chains. For instance, water 2005 is in contact with chain B and is equivalent to waters 1005, 3005, 4005, and 5005 (chains A, C, D, and E respectively.) The relatively low number, 5, indicates tht these waters have a rather high density.
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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