+Open data
-Basic information
Entry | Database: PDB / ID: 6y7e | |||||||||
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Title | Pseudomonas stutzeri nitrous oxide reductase mutant, H494A | |||||||||
Components | Nitrous-oxide reductase | |||||||||
Keywords | OXIDOREDUCTASE / periplasmic copper-binding protein | |||||||||
Function / homology | Function and homology information nitrous-oxide reductase / nitrous-oxide reductase activity / copper ion import / denitrification pathway / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane Similarity search - Function | |||||||||
Biological species | Pseudomonas stutzeri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Zhang, L. / Kroneck, P.M.H. / Einsle, O. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Chem Sci / Year: 2021 Title: A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase. Authors: Zhang, L. / Bill, E. / Kroneck, P.M.H. / Einsle, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y7e.cif.gz | 493.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y7e.ent.gz | 399.9 KB | Display | PDB format |
PDBx/mmJSON format | 6y7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y7e_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 6y7e_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 6y7e_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 6y7e_validation.cif.gz | 80 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/6y7e ftp://data.pdbj.org/pub/pdb/validation_reports/y7/6y7e | HTTPS FTP |
-Related structure data
Related structure data | 6y6yC 6y71C 6y72C 6y77C 6y7dC 7aqaC 3sbqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 71891.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosZ / Production host: Escherichia coli (E. coli) / References: UniProt: P19573, nitrous-oxide reductase |
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-Non-polymers , 9 types, 1112 molecules
#2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-CA / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | 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 Å3/Da / Density % sol: 38.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M bis-tris propane buffer at pH 8.5, 0.1 M sodium formate, 0.1 M sodium chloride, and 25% (w/v) of a medium molecular weight (MMW) polyethylene glycol mixture (PEG 2K, 3350, 4K and 5K MME) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.36999 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.36999 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→108.3 Å / Num. obs: 110732 / % possible obs: 91.7 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.6→1.74 Å / Num. unique obs: 5531 / CC1/2: 0.624 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3sbq Resolution: 1.6→108.3 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 168.18 Å2 / Biso min: 10.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→108.3 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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