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Yorodumi- PDB-2afn: STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AND A COPPER ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2afn | |||||||||
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Title | STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AND A COPPER SITE MUTANT, M150E, THAT CONTAINS ZINC | |||||||||
Components | NITRITE REDUCTASE | |||||||||
Keywords | OXIDOREDUCTASE (NITRIC OXIDE(A)) / OXIDOREDUCTASE / (NITRIC OXIDE (A)) / COPPER / FLAVOPROTEIN / FAD / NITRITE 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 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 | 2afn.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2afn.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 2afn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/2afn ftp://data.pdbj.org/pub/pdb/validation_reports/af/2afn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | NITRITE REDUCTASE IS A FUNCTIONAL TRIMER. |
-Components
#1: Protein | Mass: 37063.887 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: S-6 / References: UniProt: P38501, EC: 1.7.99.3 #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE |
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→85 Å / Num. obs: 55751 / % possible obs: 84.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.051 |
Reflection | *PLUS % possible obs: 85 % |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.25 Å / % possible obs: 69 % / Redundancy: 2.3 % / Num. unique obs: 13333 / Rmerge(I) obs: 0.154 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / σ(F): 3
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Displacement parameters | Biso mean: 24.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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