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Yorodumi- PDB-5i5m: Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstitu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i5m | |||||||||
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Title | Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstituted form | |||||||||
Components | Nitrous-oxide reductase | |||||||||
Keywords | OXIDOREDUCTASE / nitrogen cycle nitrous oxide reductase beta-propeller apoprotein | |||||||||
Function / homology | Function and homology information nitrous-oxide reductase / nitrous-oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane Similarity search - Function | |||||||||
Biological species | Shewanella denitrificans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Schneider, L.K. / Einsle, O. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase. Authors: Schneider, L.K. / Einsle, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i5m.cif.gz | 264.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i5m.ent.gz | 208.6 KB | Display | PDB format |
PDBx/mmJSON format | 5i5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i5m_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
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Full document | 5i5m_full_validation.pdf.gz | 480.5 KB | Display | |
Data in XML | 5i5m_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 5i5m_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/5i5m ftp://data.pdbj.org/pub/pdb/validation_reports/i5/5i5m | HTTPS FTP |
-Related structure data
Related structure data | 5i5iSC 5i5jC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 71172.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013) (bacteria) Gene: nosZ, Sden_2219 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12M27, nitrous-oxide reductase #2: Chemical | #3: Chemical | ChemComp-BU3 / ( #4: Chemical | #5: 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: 1.97 Å3/Da / Density % sol: 37.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25 % PEG 3350 0.2 M ammonium sulfate 0.1 M Bis-tris/HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2015 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→47.35 Å / Num. obs: 219234 / % possible obs: 99.3 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 13.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5i5i Resolution: 1.37→157.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.529 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.597 Å2
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Refinement step | Cycle: 1 / Resolution: 1.37→157.52 Å
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Refine LS restraints |
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