[English] 日本語
Yorodumi- PDB-1ly9: The impact of the physical and chemical environment on the molecu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ly9 | ||||||
---|---|---|---|---|---|---|---|
Title | The impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase | ||||||
Components | Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / mutant / thermostability / Coprinus cinereus | ||||||
Function / homology | Function and homology information lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Coprinopsis cinerea (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Houborg, K. / Harris, P. / Petersen, J.F.W. / Rowland, P. / Poulsen, J.-C.N. / Schneider, P. / Vind, J. / Larsen, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase. Authors: Houborg, K. / Harris, P. / Petersen, J. / Rowland, P. / Poulsen, J.C. / Schneider, P. / Vind, J. / Larsen, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ly9.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ly9.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ly9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1ly9 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1ly9 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35578.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: CIP1 / Production host: Aspergillus oryzae (mold) / References: UniProt: P28314, peroxidase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.25 Details: 1.8M NH4H2PO4, pH 4.00-4.50, VAPOR DIFFUSION, HANGING DROP at 293K, pH 4.25 | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / PH range low: 4.5 / PH range high: 4 | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 18, 1996 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→32 Å / Num. all: 44226 / Num. obs: 40199 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.21 / Rsym value: 0.21 / % possible all: 74.2 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 29 Å / Num. measured all: 73087 |
Reflection shell | *PLUS % possible obs: 74.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.01 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4263 Å2 / ksol: 0.327321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.227 |