[English] 日本語
Yorodumi- PDB-1rzp: Crystal Structure of C-Terminal Despentapeptide Nitrite Reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of C-Terminal Despentapeptide Nitrite Reductase from Achromobacter Cycloclastes at pH6.2 | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / denitrification / residue deletion / pH profile / Greek key beta barrel | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Li, H.T. / Wang, C. / Chang, T. / Chang, W.C. / Liu, M.Y. / Le Gall, J. / Gui, L.L. / Zhang, J.P. / An, X.M. / Chang, W.R. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes Authors: Li, H.T. / Wang, C. / Chang, T. / Chang, W.C. / Liu, M.Y. / Le Gall, J. / Gui, L.L. / Zhang, J.P. / An, X.M. / Chang, W.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rzp.cif.gz | 219 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rzp.ent.gz | 172.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzp ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzp | HTTPS FTP |
---|
-Related structure data
Related structure data | 1rzqC 1niaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a trimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 36544.160 Da / Num. of mol.: 3 / Fragment: C-Terminal Despentapeptide Nitrite Reductase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): M15(PREP4) / References: UniProt: P25006, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.69 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.6M ammonium sulfate, 0.1M Mes, 0.2M sodium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 113326 / Num. obs: 112590 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.9 / % possible all: 98.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NIA Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
|