[English] 日本語
Yorodumi- PDB-1n50: FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n50 | ||||||
---|---|---|---|---|---|---|---|
Title | FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NITRITE REDUCTASE / PSEUDOMONAS AERUGINOSA / HEMOPROTEIN / DENITRIFICATION / CONFORMATIONAL CHANGE / MICROSPECTROPHOTOMETRY | ||||||
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 / Resolution: 2.9 Å | ||||||
Authors | Nurizzo, D. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Does the reduction of c heme trigger the conformational change of crystalline nitrite reductase? Authors: Nurizzo, D. / Cutruzzola, F. / Arese, M. / Bourgeois, D. / Brunori, M. / Cambillau, C. / Tegoni, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n50.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n50.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n50 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n50 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60259.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MODEL WITHOUT ION AND WATER / Source: (natural) Pseudomonas aeruginosa (bacteria) / Cellular location: PERIPLASMIC SPACEPeriplasm / References: UniProt: P24474, EC: 1.9.3.2 #2: Chemical | #3: Chemical | Nonpolymer details | ABOUT 50% OF THE C HEMES ARE REDUCED D1 HEMES ARE FULLY OXIDIZED DETERMINED BY ...ABOUT 50% OF THE C HEMES ARE REDUCED D1 HEMES ARE FULLY OXIDIZED DETERMINED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.56 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.2 / Details: pH 7.2 | |||||||||||||||
Crystal grow | *PLUS pH: 8.4 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. obs: 43791 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 53.6 Å2 / Rsym value: 0.067 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.75→2.82 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.345 / % possible all: 98 |
Reflection | *PLUS Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.345 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: OXIDIZED NITRITE REDUCTASE FROM PS. AERUGINOSA Resolution: 2.9→12 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 40000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.03 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|