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Open data
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Basic information
Entry | Database: PDB / ID: 2npx | |||||||||
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Title | NADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE | |||||||||
![]() | NADH PEROXIDASE | |||||||||
![]() | OXIDOREDUCTASE(H2O2(A)) | |||||||||
Function / homology | ![]() NADH peroxidase / NADH peroxidase activity / flavin adenine dinucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Stehle, T. / Claiborne, A. / Schulz, G.E. | |||||||||
![]() | ![]() Title: NADH binding site and catalysis of NADH peroxidase. Authors: Stehle, T. / Claiborne, A. / Schulz, G.E. #1: ![]() Title: The Structure of Nadh Peroxidase from Streptococcus Faecalis 10C1 Refined at 2.16 Angstroms Resolution Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E. #2: ![]() Title: The Structure of Nadh Peroxidase from Streptococcus Faecalis at 3.3 Angstroms Resolution Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.3 KB | Display | ![]() |
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PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 947.1 KB | Display | ![]() |
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Full document | ![]() | 960.8 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUE CYS 42 IS A SULFONIC ACID (CYS42-SO3H). | ||||||||
Components on special symmetry positions |
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Components
#1: Protein | Mass: 49651.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
Compound details | THE STRUCTURE IS A COMPLEX BETWEEN NADH PEROXIDASE AND ITS SUBSTRATE NADH. THE ENZYME IS IN A NON- ...THE STRUCTURE IS A COMPLEX BETWEEN NADH PEROXIDASE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20-24 ℃ / pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 27682 / % possible obs: 95.4 % / Rmerge(I) obs: 0.071 |
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Processing
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Refinement | Rfactor Rwork: 0.159 / Rfactor obs: 0.159 / Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.4 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor obs: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |