+Open data
-Basic information
Entry | Database: PDB / ID: 7aq5 | |||||||||
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Title | Pseudomonas stutzeri nitrous oxide reductase mutant, H583N | |||||||||
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: 1.7 Å | |||||||||
Authors | Zhang, L. / Bill, E. / Kroneck, P.M.H. / Einsle, O. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Histidine-Gated Proton-Coupled Electron Transfer to the Cu A 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 | 7aq5.cif.gz | 503.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aq5.ent.gz | 411 KB | Display | PDB format |
PDBx/mmJSON format | 7aq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aq5_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7aq5_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7aq5_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 7aq5_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aq5 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aq5 | HTTPS FTP |
-Related structure data
Related structure data | 7apyC 7aq0C 7aq2C 7aq3C 7aq4C 7aq6C 7aq7C 7aq8C 7aq9C 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: 71934.508 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, 727 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FMT / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-TRS / | #10: Chemical | ChemComp-K / | #11: Chemical | ChemComp-CUZ / ( | #12: 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: 2.01 Å3/Da / Density % sol: 38.87 % |
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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: 1.36998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.36998 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→62.647 Å / Num. obs: 98286 / % possible obs: 94.4 % / Redundancy: 6.6 % / CC1/2: 0.993 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.705→1.853 Å / Num. unique obs: 4915 / CC1/2: 0.383 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6rkz Resolution: 1.7→62.647 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 25.3 / 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: 109.58 Å2 / Biso mean: 39.5462 Å2 / Biso min: 15.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→62.647 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 / Origin x: 14.334 Å / Origin y: 10.2548 Å / Origin z: 26.9091 Å
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Refinement TLS group |
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