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Yorodumi- PDB-1nno: CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nno | ||||||
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Title | CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NITRITE REDUCTASE / PSEUDOMONAS AERUGINOSA / HEMOPROTEIN / DENITRIFICATION / NO BINDING / CONFORMATIONAL CHANGES | ||||||
Function / homology | Function and homology information hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.65 Å | ||||||
Authors | Nurizzo, D. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Conformational changes occurring upon reduction and NO binding in nitrite reductase from Pseudomonas aeruginosa. Authors: Nurizzo, D. / Cutruzzola, F. / Arese, M. / Bourgeois, D. / Brunori, M. / Cambillau, C. / Tegoni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nno.cif.gz | 212.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nno.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/1nno ftp://data.pdbj.org/pub/pdb/validation_reports/nn/1nno | 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: (Code: given Matrix: (0.999943, -0.001407, -0.010572), Vector: |
-Components
#1: Protein | Mass: 60259.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: EACH SUBUNIT (A,B) LINKS ONE NITRIC OXIDE (NO) AT THE CATALYTIC SITE Source: (natural) Pseudomonas aeruginosa (bacteria) / Cellular location: PERIPLASMIC SPACEPeriplasm / References: UniProt: P24474, EC: 1.9.3.2 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 3.47 Å3/Da / Density % sol: 64.6 % | |||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS pH: 8.4 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.907 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.907 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→15 Å / Num. obs: 44045 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.65→2.71 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.1 / % possible all: 93.3 |
Reflection | *PLUS Num. measured all: 361716 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 93.3 % / Rmerge(I) obs: 0.569 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.65→15 Å / Rfactor Rfree error: 0.0052 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters |
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Refine analyze | Luzzati d res low obs: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.77 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2438 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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