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Yorodumi- PDB-1zyn: Oxidized structure of the N-terminal domain of Salmonella typhimu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zyn | ||||||
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Title | Oxidized structure of the N-terminal domain of Salmonella typhimurium AhpF | ||||||
Components | Alkyl hydroperoxide reductase subunit F | ||||||
Keywords | OXIDOREDUCTASE / thiolate | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / alkyl hydroperoxide reductase activity / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / response to reactive oxygen species / NAD binding / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Roberts, B.R. / Wood, Z.A. / Jonsson, T.J. / Poole, L.B. / Karplus, P.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF Authors: Roberts, B.R. / Wood, Z.A. / Jonsson, T.J. / 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 | 1zyn.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zyn.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1zyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zyn_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 1zyn_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 1zyn_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1zyn_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/1zyn ftp://data.pdbj.org/pub/pdb/validation_reports/zy/1zyn | HTTPS FTP |
-Related 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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-Components
#1: Protein | Mass: 22317.385 Da / Num. of mol.: 2 / Fragment: residues 1-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: ahpF / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P19480, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 30-35% PEG 4000, 0.2M ammonium acetate, 0.1M Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22423 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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