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Yorodumi- PDB-2p80: Solution structure of the complex between nitrite reductase and p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p80 | ||||||
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Title | Solution structure of the complex between nitrite reductase and pseudoazurin from A. faecalis | ||||||
Components |
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Keywords | OXIDOREDUCTASE / transient complex / protein-protein interaction / redox partners / electron transfer | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | SOLUTION NMR / distance geometry, rigid body molecular dynamics, restrained side-chains energy minimization | ||||||
Authors | Vlasie, M.D. / Ubbink, M. | ||||||
Citation | Journal: To be Published Title: Low resolution solution structure of the 152 kDa complex between nitrite reductase and pseudoazurin from A. faecalis by paramagnetic NMR. Authors: Vlasie, M.D. / Fernandez-Busnadiego, R. / Prudencio, M. / Ubbink, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p80.cif.gz | 7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2p80.ent.gz | 5.9 MB | Display | PDB format |
PDBx/mmJSON format | 2p80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p80_validation.pdf.gz | 403.7 KB | Display | wwPDB validaton report |
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Full document | 2p80_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2p80_validation.xml.gz | 686.8 KB | Display | |
Data in CIF | 2p80_validation.cif.gz | 967.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/2p80 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/2p80 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 36878.648 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Gene: nirK, nir / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P38501, nitrite reductase (NO-forming) #2: Protein | | Mass: 13383.511 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04377 #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-GD / |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 15N,1H TROSY |
NMR details | Text: ~80% deuteration of the nonexchangeable protons in pseudoazurin |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry, rigid body molecular dynamics, restrained side-chains energy minimization Software ordinal: 1 Details: 324 distance restraints from paramagnetic relaxation, 5 restraints from chemical shift perturbations | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures closest to the average Conformers calculated total number: 134 / Conformers submitted total number: 20 |