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Yorodumi- PDB-7qq2: CRYSTAL STRUCTURE OF AS-ISOLATED S321M MUTANT OF THREE-DOMAIN HEM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qq2 | ||||||
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Title | CRYSTAL STRUCTURE OF AS-ISOLATED S321M 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Petchyam, N. / Antonyuk, S. / Hasnain, S.S. | ||||||
Funding support | United Kingdom, 1items
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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 | 7qq2.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qq2.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qq2_validation.pdf.gz | 766.7 KB | Display | wwPDB validaton report |
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Full document | 7qq2_full_validation.pdf.gz | 768.9 KB | Display | |
Data in XML | 7qq2_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7qq2_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qq2 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qq2 | HTTPS FTP |
-Related structure data
Related structure data | 8qgfC 3ziyS S: Starting model for refinement 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: 49992.633 Da / Num. of mol.: 1 / Mutation: S321M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia pickettii (bacteria) / Gene: RP6297_03937 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: I6NAW4, nitrite reductase (NO-forming) | ||||||
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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 grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020 / Details: MIRRORS | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9126 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.1→73.65 Å / Num. obs: 56514 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.06 / Rrim(I) all: 0.129 / Net I/av σ(I): 8.1 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZIY Resolution: 2.1→73.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.997 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 109.56 Å2 / Biso mean: 34.351 Å2 / Biso min: 11.4 Å2
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Refinement step | Cycle: final / Resolution: 2.1→73.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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