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Yorodumi- PDB-8qgf: CRYSTAL STRUCTURE OF AS-ISOLATED M148L MUTANT OF THREE-DOMAIN HEM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qgf | |||||||||
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Title | CRYSTAL STRUCTURE OF AS-ISOLATED M148L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII | |||||||||
Components | Copper-containing nitrite reductase | |||||||||
Keywords | OXIDOREDUCTASE / HAEM AND CU CONTAINING NITRITE REDUCTASE / ELECTRON TRANSFER / REDOX REACTIONS / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Ralstonia pickettii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å | |||||||||
Authors | Petchyam, N. / Antonyuk, S. / Hasnain, S.S. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qgf.cif.gz | 405 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qgf.ent.gz | 331.7 KB | Display | PDB format |
PDBx/mmJSON format | 8qgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qgf_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8qgf_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8qgf_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 8qgf_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/8qgf ftp://data.pdbj.org/pub/pdb/validation_reports/qg/8qgf | HTTPS FTP |
-Related structure data
Related structure data | 7qq2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 48597.957 Da / Num. of mol.: 1 / Mutation: M148L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia pickettii (bacteria) / Plasmid: pET26b-M148L_RpNiR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NAW4 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEC / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-tris propane pH 6.3, 0.1 M sodium citrate, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→46.66 Å / Num. obs: 124091 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.067 / Rrim(I) all: 0.152 / Χ2: 0.98 / Net I/av σ(I): 6.4 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.888 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5450 / CC1/2: 0.265 / Rpim(I) all: 0.961 / Rrim(I) all: 2.124 / Χ2: 0.97 / % possible all: 87.9 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.32→46.66 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.199 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.23 Å2
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Refinement step | Cycle: 1 / Resolution: 1.32→46.66 Å
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