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Yorodumi- PDB-4ysq: Structure of copper nitrite reductase from Geobacillus thermodeni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ysq | ||||||
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Title | Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 8.38 MGy | ||||||
Components | Nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / Nitrite / Copper / Reductase | ||||||
Function / homology | Function and homology information nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. ...Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Matsumura, H. / Inoue, T. / Iwata, S. / Mizohata, E. | ||||||
Citation | Journal: J.Biochem. / Year: 2016 Title: Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography Authors: Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / ...Authors: Fukuda, Y. / Tse, K.M. / Suzuki, M. / Diederichs, K. / Hirata, K. / Nakane, T. / Sugahara, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Song, C. / Hatsui, T. / Yabashi, M. / Nureki, O. / Matsumura, H. / 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 | 4ysq.cif.gz | 148.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ysq.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ysq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ysq_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 4ysq_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 4ysq_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 4ysq_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/4ysq ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ysq | HTTPS FTP |
-Related structure data
Related structure data | 4ysaC 4ysdC 4ysoC 4yspC 4ysrC 4yssC 4ystC 4ysuC 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: 35523.062 Da / Num. of mol.: 1 / Fragment: UNP residues 31-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria) Strain: NG80-2 / Gene: nirK, GTNG_0650 / Plasmid: pET22b / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4IL26 | ||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-MPD / ( | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate, 5.5%(w/v) PEG 4000, 0.075M CuSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.75 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 64868 / % possible obs: 96.6 % / Redundancy: 2.9 % / Net I/σ(I): 11.2 |
-Processing
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Refinement | Resolution: 1.5→34.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.069 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.561 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→34.35 Å
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