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Yorodumi- PDB-1n8j: Crystal Structure of AhpC with Active Site Cysteine mutated to Se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n8j | ||||||
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Title | Crystal Structure of AhpC with Active Site Cysteine mutated to Serine (C46S) | ||||||
Components | Alkyl hydroperoxide reductase C22 protein | ||||||
Keywords | OXIDOREDUCTASE / AhpC / peroxiredoxin / decamer / antioxidant / peroxidase / alkylhydroperoxide reductase / AhpF | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Wood, Z.A. / Poole, L.B. / Karplus, P.A. | ||||||
Citation | Journal: Science / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n8j.cif.gz | 736.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n8j.ent.gz | 613.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n8j_validation.pdf.gz | 577.6 KB | Display | wwPDB validaton report |
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Full document | 1n8j_full_validation.pdf.gz | 653.1 KB | Display | |
Data in XML | 1n8j_validation.xml.gz | 147.4 KB | Display | |
Data in CIF | 1n8j_validation.cif.gz | 202.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n8j ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n8j | HTTPS FTP |
-Related structure data
Related structure data | 1kyg 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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2 |
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Unit cell |
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Details | The biological assembly is a decamer made up of chains A,B,C,D,E,F,G,H,I,J or K,L,M,N,O,P,Q,R,S,T |
-Components
#1: Protein | Mass: 20625.123 Da / Num. of mol.: 20 / Mutation: C46S 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: 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: 2.67 Å3/Da / Density % sol: 53.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 4% PEG 4000, 10% isopropyl alcohol, 0.1M Na acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 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: Jan 19, 2001 / Details: double crystal |
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: 2.17→19.99 Å / Num. all: 210095 / Num. obs: 210095 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.066 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.17→2.31 Å / % possible all: 74.8 |
Reflection | *PLUS Num. obs: 204205 / % possible obs: 90.4 % / Rmerge(I) obs: 0.074 / Num. measured all: 836640 |
Reflection shell | *PLUS % possible obs: 82 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KYG 1kyg Resolution: 2.17→19.99 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.3883 Å2 / ksol: 0.333622 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.17→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.31 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.187 / Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.28 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.335 |