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Yorodumi- PDB-5d4i: Intact nitrite complex of a copper nitrite reductase determined b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d4i | ||||||
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Title | Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / copper | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. ...Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Murphy, M.E.P. / Inoue, T. / Iwata, S. / Mizohata, E. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography Authors: Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, ...Authors: Fukuda, Y. / Tse, K.M. / Nakane, T. / Nakatsu, T. / Suzuki, M. / Sugahara, M. / Inoue, S. / Masuda, T. / Yumoto, F. / Matsugaki, N. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Murphy, M.E. / Inoue, T. / Iwata, S. / Mizohata, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d4i.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d4i.ent.gz | 170.7 KB | Display | PDB format |
PDBx/mmJSON format | 5d4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/5d4i ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d4i | HTTPS FTP |
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-Related structure data
Related structure data | 4yscC 4yseC 5d4hC 5d4jC 5f7aC 5f7bC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1274312 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37019.922 Da / Num. of mol.: 3 / Fragment: UNP residues 40-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: nirK, nir / Production host: Escherichia coli (E. coli) / References: UniProt: P38501, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 4 / Details: 100mM sodium acetate (pH 4.0) and 12% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: LCP injector |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.149 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.149 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.97 Å / Num. obs: 120700 / % possible obs: 100 % / Redundancy: 1079 % / Net I/σ(I): 11.87 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1021.6 % / Mean I/σ(I) obs: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.97 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.278 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→28.97 Å
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Refine LS restraints |
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