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Yorodumi- PDB-3h8l: The first X-ray structure of a sulfide:quinone oxidoreductase: in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h8l | ||||||
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Title | The first X-ray structure of a sulfide:quinone oxidoreductase: insights into sulfide oxidation mechanism | ||||||
Components | NADH oxidase | ||||||
Keywords | OXIDOREDUCTASE / Membrane protein / complete form / rossman-like fold | ||||||
Function / homology | Function and homology information bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane Similarity search - Function | ||||||
Biological species | Acidianus ambivalens (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.57 Å | ||||||
Authors | Brito, J.A. / Sousa, F.L. / Stelter, M. / Bandeiras, T.M. / Vonrhein, C. / Teixeira, M. / Pereira, M.M. / Archer, M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and functional insights into sulfide:quinone oxidoreductase. Authors: Brito, J.A. / Sousa, F.L. / Stelter, M. / Bandeiras, T.M. / Vonrhein, C. / Teixeira, M. / Pereira, M.M. / Archer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h8l.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h8l.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 3h8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h8l_validation.pdf.gz | 1009.6 KB | Display | wwPDB validaton report |
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Full document | 3h8l_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3h8l_validation.xml.gz | 33 KB | Display | |
Data in CIF | 3h8l_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/3h8l ftp://data.pdbj.org/pub/pdb/validation_reports/h8/3h8l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45174.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acidianus ambivalens (archaea) / References: UniProt: Q7ZAG8, NADH dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Sequence details | ACCORDING TO THE AUTHORS THE UNP DATABASE SEQUENCE IS IN ERROR AT THIS POSITION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.943 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.943 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→51.44 Å / Num. obs: 49511 / Observed criterion σ(I): 2.6 / Redundancy: 7.7 % / Biso Wilson estimate: 67.89 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6870 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.57→29.68 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 55.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→29.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.57→2.64 Å / Total num. of bins used: 20
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