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Yorodumi- PDB-2ms3: The NMR structure of the rubredoxin domain of the NO Reductase Fl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ms3 | ||||||
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Title | The NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli | ||||||
Components | Anaerobic nitric oxide reductase flavorubredoxin | ||||||
Keywords | ELECTRON TRANSPORT / rubredoxin / flavorubredoxin / nitric oxide reductase / nitric oxide / NorV | ||||||
Function / homology | Function and homology information nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Turner, D.L. / Silva, E. / Lamosa, P.M. / Teixeira, M. | ||||||
Citation | Journal: To be Published Title: The NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli Authors: Turner, D.L. / Silva, E. / Lamosa, P.M. / Teixeira, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ms3.cif.gz | 338.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ms3.ent.gz | 276.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ms3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ms3_validation.pdf.gz | 400.7 KB | Display | wwPDB validaton report |
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Full document | 2ms3_full_validation.pdf.gz | 567 KB | Display | |
Data in XML | 2ms3_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 2ms3_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/2ms3 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/2ms3 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6292.064 Da / Num. of mol.: 1 / Fragment: UNP residues 423-479 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) Description: The growth medium was enriched with Zn chloride and 15N-labeled ammonium sulfate Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q46877 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.1 mM [U-99% 15N] rubredoxin domain of the NO Reductase Flavorubredoxin-1, 100 mM sodium chloride-2, 10 mM potassium phosphate-3, 0.04 % sodium azide-4, 90 % H2O-5, 10 % D2O-6, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.2 / pH: 7.7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR constraints | NOE intraresidue total count: 614 / NOE long range total count: 1197 / NOE medium range total count: 539 / NOE sequential total count: 568 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.51 Å / Maximum upper distance constraint violation: 0.46 Å / Representative conformer: 1 | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.07 Å |