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Yorodumi- PDB-3wnj: 1.20 A resolution crystal structure of dioxygen bound copper-cont... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wnj | ||||||
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Title | 1.20 A resolution crystal structure of dioxygen bound copper-containing nitrite reductase from Geobacillus thermodenitrificans | ||||||
Components | Nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / Greek key beta barrel / dissimilatory nitrite reductase / periplasm-like space | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Fukuda, Y. / Inoue, T. | ||||||
Citation | Journal: To be Published Title: Crystallographic evidence for side-on dioxygen trapped on type 2 copper in copper-containing nitrite reductase Authors: Fukuda, Y. / Inoue, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wnj.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wnj.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wnj_validation.pdf.gz | 476.5 KB | Display | wwPDB validaton report |
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Full document | 3wnj_full_validation.pdf.gz | 479.6 KB | Display | |
Data in XML | 3wnj_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 3wnj_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wnj ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wnj | HTTPS FTP |
-Related structure data
Related structure data | 3wniC 3wko C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#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 (bacteria) Strain: NG80-2 / Gene: nirK / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4IL26 |
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-Non-polymers , 8 types, 375 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-OXY / | #5: Chemical | ChemComp-MPD / ( | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACY / #9: 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: 3 Å3/Da / Density % sol: 59.07 % |
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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 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→100 Å / Num. all: 120357 / Num. obs: 120357 / % possible obs: 92.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3 / Num. unique all: 6323 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WKO 3wko Resolution: 1.2→28.73 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.87 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.03 / 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: 15.588 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→28.73 Å
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Refine LS restraints |
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