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Yorodumi- PDB-1xdy: Structural and Biochemical Identification of a Novel Bacterial Ox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xdy | ||||||
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Title | Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor | ||||||
Components | Bacterial Sulfite Oxidase | ||||||
Keywords | OXIDOREDUCTASE / Bioinformatics / sequence analysis / electron transfer / molybdoenzymes / molybdopterin | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on a heme group of donors / response to hypochlorite / oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / protein repair / molybdopterin cofactor binding / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Loschi, L. / Brokx, S.J. / Hills, T.L. / Zhang, G. / Bertero, M.G. / Lovering, A.L. / Weiner, J.H. / Strynadka, N.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural and biochemical identification of a novel bacterial oxidoreductase. Authors: Loschi, L. / Brokx, S.J. / Hills, T.L. / Zhang, G. / Bertero, M.G. / Lovering, A.L. / Weiner, J.H. / Strynadka, N.C. | ||||||
History |
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Remark 999 | SEQUENCE The authors believe that there is an an error in the database sequence since the other E. ...SEQUENCE The authors believe that there is an an error in the database sequence since the other E.coli strains with published sequences like the pathogenic strains O157:H7 EDL933, and CFT073 also have an Asp at that position. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xdy.cif.gz | 535.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xdy.ent.gz | 437.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xdy_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
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Full document | 1xdy_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 1xdy_validation.xml.gz | 104.7 KB | Display | |
Data in CIF | 1xdy_validation.cif.gz | 136.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/1xdy ftp://data.pdbj.org/pub/pdb/validation_reports/xd/1xdy | HTTPS FTP |
-Related structure data
Related structure data | 1xdqSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 33666.258 Da / Num. of mol.: 10 / Fragment: residues 45-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Plasmid details: plasmid pMSYZ3 (construcy with YedYZ cloned) which is derived from plasmid pMS119 Plasmid: pMSYZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 and SBJ20 / References: UniProt: P76342 #2: Chemical | ChemComp-W / #3: Chemical | ChemComp-MTE / #4: 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: 2.2 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG3350, Magnesium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.54 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2004 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 146127 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.4 Å2 |
Reflection shell | Resolution: 2.2→2.31 Å / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XDQ Resolution: 2.2→38.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2806313.85 / Data cutoff low absF: 0 / 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: 35.0442 Å2 / ksol: 0.307329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→38.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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