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Yorodumi- PDB-1npx: STRUCTURE OF NADH PEROXIDASE FROM STREPTOCOCCUS FAECALIS 10C1 REF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1npx | ||||||
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Title | STRUCTURE OF NADH PEROXIDASE FROM STREPTOCOCCUS FAECALIS 10C1 REFINED AT 2.16 ANGSTROMS RESOLUTION | ||||||
Components | NADH PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE(H2O2(A)) | ||||||
Function / homology | Function and homology information NADH peroxidase / NADH peroxidase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.16 Å | ||||||
Authors | Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 A resolution. Authors: Stehle, T. / Ahmed, S.A. / Claiborne, A. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Cloning, Sequence and Overexpression of Nadh Peroxidase from Streptococcus Faecalis 10C1. Structural Relationship with the Flavoprotein Disulfide Reductases Authors: Ross, R.P. / Claiborne, A. #2: Journal: FEBS Lett. / Year: 1990 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. #3: Journal: J.Biol.Chem. / Year: 1989 Title: The Non-Flavin Redox Center of the Streptococcal Nadh Peroxidase. II. Evidence for a Stabilized Cysteine-Sulfenic Acid Authors: Poole, L.B. / Claiborne, A. #4: Journal: J.Biol.Chem. / Year: 1989 Title: The Non-Flavin Redox Center of the Streptococcal Nadh Peroxidase. I. Thiol Reactivity and Redox Behavior in the Presence of Urea Authors: Poole, L.B. / Claiborne, A. #5: Journal: J.Biol.Chem. / Year: 1986 Title: Interactions of Pyridine Nucleotides with Redox Forms of the Flavin-Containing Nadh Peroxidase from Streptococcus Faecalis Authors: Poole, L.B. / Claiborne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1npx.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1npx.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 1npx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npx ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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). 2: DISCRETE DISORDER IS OBSERVED FOR SOME SIDE-CHAINS ATOMS OF RESIDUES ASP 25, LYS 51, ASP 124, AND ARG 447. | ||||||||
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.) Enterococcus faecalis (bacteria) / References: UniProt: P37062, NADH peroxidase |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.16 Å / Lowest resolution: 9999 Å / Num. obs: 37857 / % possible obs: 92 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Highest resolution: 2.16 Å / Lowest resolution: 2.2 Å / % possible obs: 77 % |
-Processing
Software |
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Refinement | Resolution: 2.16→7 Å / Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.16 Å / Lowest resolution: 7 Å / Num. reflection all: 36563 / σ(F): 0 / Rfactor all: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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