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- PDB-7r2u: CRYSTAL STRUCTURE OF AS-ISOLATED Q262N MUTANT OF THREE-DOMAIN HEM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r2u | |||||||||
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Title | CRYSTAL STRUCTURE OF AS-ISOLATED Q262N MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII | |||||||||
![]() | Copper-containing nitrite reductase | |||||||||
![]() | OXIDOREDUCTASE / HAEM AND CU CONTAINING NITRITE REDUCTASE / ELECTRON TRANSFER / REDOX REACTIONS / METAL BINDING PROTEIN | |||||||||
Function / homology | ![]() nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Petchyam, N. / Antonyuk, S. / Hasnain, S.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical studies of three-domain haem CuNiR from Ralstonia pickettii mutants Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 415.2 KB | Display | ![]() |
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PDB format | ![]() | 342.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.8 KB | Display | ![]() |
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Full document | ![]() | 814.5 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ziyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 49934.488 Da / Num. of mol.: 1 / Mutation: Q262N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEC / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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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% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2021 / Details: Mirrors | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→37.63 Å / Num. obs: 83956 / % possible obs: 100 % / Redundancy: 5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.054 / Rrim(I) all: 0.121 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZIY Resolution: 1.5→37.63 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.976 / SU B: 3.455 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 100.43 Å2 / Biso mean: 24.346 Å2 / Biso min: 10.83 Å2
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Refinement step | Cycle: final / Resolution: 1.5→37.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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