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Yorodumi- PDB-1nib: THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nib | ||||||
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Title | THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE (NITRIC OXIDE(A)) | ||||||
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 | Achromobacter cycloclastes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Adman, E.T. / Godden, J.W. / Turley, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1995 Title: The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted. Authors: Adman, E.T. / Godden, J.W. / Turley, S. #1: 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. #2: Journal: Biochemistry / Year: 1991 Title: Amino Acid Sequence of Nitrite Reductase: A Copper Protein from Achromobacter Cycloclastes Authors: Fenderson, F.F. / Kumar, S. / Adman, E.T. / Liu, M.-Y. / Payne, W.J. / Legall, J. #3: Journal: J.Mol.Biol. / Year: 1988 Title: Crystallization of Nitrite Reductase from Achromobacter Cycloclastes Authors: Turley, S. / Adman, E.T. / Sieker, L.C. / 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 | 1nib.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nib.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1nib ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1nib | HTTPS FTP |
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-Related structure data
Related structure data | 1niaC 1nicC 1nidC 1nieC 1nifC 2nrdC 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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Atom site foot note | 1: CIS PROLINE - PRO A 23 / 2: CIS PROLINE - PRO A 69 / 3: CIS PROLINE - PRO B 23 / 4: CIS PROLINE - PRO B 69 / 5: CIS PROLINE - PRO C 23 / 6: CIS PROLINE - PRO C 69 | ||||||||
Details | THE TRIMER PRESENTED IN THIS ENTRY IS THE ASYMMETRIC UNIT. |
-Components
#1: Protein | Mass: 37059.809 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: PH 6.8 ("68") / Source: (natural) Achromobacter cycloclastes (bacteria) / References: UniProt: P25006, EC: 1.7.99.3 #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | Nonpolymer details | NOTE THAT A NUMBER OF WATERS HAVE OCCUPANCY GREATER THAN 1.0. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.81 % | |||||||||||||||
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Crystal grow | pH: 6.8 / Details: pH 6.8 | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | Highest resolution: 2.6 Å / Num. obs: 37413 / % possible obs: 85 % / Observed criterion σ(I): 0 |
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Reflection | *PLUS Lowest resolution: 9999 Å / Rmerge(I) obs: 0.117 |
Reflection shell | *PLUS Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 2.7→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |