+Open data
-Basic information
Entry | Database: PDB / ID: 7aqa | |||||||||
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Title | Pseudomonas stutzeri nitrous oxide reductase mutant, H382A | |||||||||
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: 1.497 Å | |||||||||
Authors | Zhang, L. / Bill, E. / 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 | 7aqa.cif.gz | 493.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqa.ent.gz | 400.8 KB | Display | PDB format |
PDBx/mmJSON format | 7aqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqa_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 7aqa_full_validation.pdf.gz | 475 KB | Display | |
Data in XML | 7aqa_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 7aqa_validation.cif.gz | 81.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqa ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqa | HTTPS FTP |
-Related structure data
Related structure data | 6y6yC 6y71C 6y72C 6y77C 6y7dC 6y7eC 6rkzS 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 BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P19573, nitrous-oxide reductase |
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-Non-polymers , 11 types, 1104 molecules
#2: Chemical | ChemComp-K7E / | ||||||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PHE / | #10: Chemical | ChemComp-RUQ / ( | #11: Chemical | ChemComp-FMT / | #12: Water | ChemComp-HOH / | |
-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: 1.99 Å3/Da / Density % sol: 38.25 % |
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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: X06SA / Wavelength: 1.369991 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.369991 Å / Relative weight: 1 |
Reflection | Resolution: 1.497→108.315 Å / Num. obs: 116124 / % possible obs: 86.6 % / Redundancy: 7.4 % / CC1/2: 0.999 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.497→1.644 Å / Num. unique obs: 5792 / CC1/2: 0.669 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6rkz Resolution: 1.497→62.668 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 25.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.82 Å2 / Biso mean: 29.4773 Å2 / Biso min: 9.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.497→62.668 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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