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Yorodumi- PDB-1ntd: STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE MUTANT M150E ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ntd | ||||||
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Title | STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE MUTANT M150E THAT CONTAINS ZINC | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE (NITRIC OXIDE(A)) / OXIDOREDUCTASE / FLAVOPROTEIN / FAD / NITRATE ASSIMILATION | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Murphy, M.E.P. / Adman, E.T. / Turley, S. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc. Authors: Murphy, M.E. / Turley, S. / Kukimoto, M. / Nishiyama, M. / Horinouchi, S. / Sasaki, H. / Tanokura, M. / Adman, E.T. #1: Journal: Biochemistry / Year: 1994 Title: X-Ray Structure and Site-Directed Mutagenesis of a Nitrite Reductase from Alcaligenes Faecalis S-6; Roles of Two Copper Atoms in Nitrite Reduction Authors: Kukimoto, M. / Nishiyama, M. / Murphy, M.E. / Turley, S. / Adman, E.T. / Horinouchi, S. / Beppu, T. #2: Journal: Science / Year: 1991 Title: The 2.3 Angstrom X-Ray Structure of Nitrite Reductase from Achromobacter Cycloclastes Authors: Godden, J.W. / Turley, S. / Teller, D.C. / Adman, E.T. / Liu, M.Y. / Payne, W.J. / Legall, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ntd.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ntd.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ntd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ntd_validation.pdf.gz | 415.4 KB | Display | wwPDB validaton report |
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Full document | 1ntd_full_validation.pdf.gz | 417.5 KB | Display | |
Data in XML | 1ntd_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1ntd_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1ntd ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1ntd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | NITRITE REDUCTASE IS A FUNCTIONAL TRIMER. |
-Components
#1: Protein | Mass: 37061.805 Da / Num. of mol.: 1 / Mutation: M150E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: STRAIN S-6 / Gene: NIR / Plasmid: PNIR601 / Gene (production host): NIR / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P38501, EC: 1.7.99.3 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 17281 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 90 % / Redundancy: 1.6 % / Num. unique obs: 4167 / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 5.1 |
-Processing
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Refinement | Resolution: 2.3→10 Å / σ(F): 3
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Displacement parameters | Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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