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Yorodumi- PDB-1as6: STRUCTURE OF NITRITE BOUND TO OXIDIZED ALCALIGENES FAECALIS NITRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1as6 | ||||||
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Title | STRUCTURE OF NITRITE BOUND TO OXIDIZED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NITRITE / COPPER / DENITRIFICATION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Murphy, M.E.P. / Adman, E.T. / Turley, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications. Authors: Murphy, M.E. / Turley, S. / Adman, E.T. #1: 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. #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 | 1as6.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1as6.ent.gz | 223.4 KB | Display | PDB format |
PDBx/mmJSON format | 1as6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1as6_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 1as6_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 1as6_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 1as6_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/1as6 ftp://data.pdbj.org/pub/pdb/validation_reports/as/1as6 | HTTPS FTP |
-Related structure data
Related structure data | 1aq8C 1as7C 1as8C 2afnS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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-Components
#1: Protein | Mass: 37063.887 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Cellular location: PERIPLASM / Plasmid: PNIR701 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM-105 / References: UniProt: P38501, EC: 1.7.99.3 #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: 10% PEG4000, 0.1 SODIUM ACETATE PH 4.5 | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 4.8 / PH range high: 4 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 2, 1995 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 70076 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 3.9 / % possible all: 0.44 |
Reflection shell | *PLUS % possible obs: 44 % / Num. unique obs: 10128 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AFN Resolution: 1.8→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 0 /
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Displacement parameters | Biso mean: 19.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.98 Å / Total num. of bins used: 8 /
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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