[English] 日本語
Yorodumi- PDB-1aoq: CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aoq | ||||||
---|---|---|---|---|---|---|---|
Title | CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ENZYME / NITRITE REDUCTASE | ||||||
Function / homology | Function and homology information hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Paracoccus pantotrophus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Williams, P.A. / Fulop, V. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. Authors: Williams, P.A. / Fulop, V. / Garman, E.F. / Saunders, N.F. / Ferguson, S.J. / Hajdu, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1aoq.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1aoq.ent.gz | 202.1 KB | Display | PDB format |
PDBx/mmJSON format | 1aoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aoq_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1aoq_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1aoq_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 1aoq_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/1aoq ftp://data.pdbj.org/pub/pdb/validation_reports/ao/1aoq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.71811, 0.540276, 0.438658), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62605.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus pantotrophus (bacteria) / Cellular location: PERIPLASM / References: UniProt: P72181 |
---|
-Non-polymers , 5 types, 1114 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-2NO / | #5: Chemical | ChemComp-NO / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
---|---|
Crystal grow | pH: 7 Details: 2.3 M AMMONIUM SULFATE 50MM POTASSIUM PHOSPHATE PH 7.0 CRYSTALS WERE REDUCED USING 16MM SODIUM DITHIONITE. CRYSTAL 2 SOAKED IN NITRITE. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.88 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 101329 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Rsym value: 0.029 |
Reflection shell | Resolution: 1.8→1.86 Å / Rsym value: 0.072 / % possible all: 88.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 303438 / Rmerge(I) obs: 0.029 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→30 Å / Rfactor Rfree error: 0.0031 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 20
| ||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |