[English] 日本語
Yorodumi- PDB-2ih8: A low-dose crystal structure of a recombinant Melanocarpus albomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ih8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A low-dose crystal structure of a recombinant Melanocarpus albomyces laccase | |||||||||
Components | Laccase-1 | |||||||||
Keywords | OXIDOREDUCTASE / laccase / multicopper oxidase / redox-enzyme | |||||||||
Function / homology | Function and homology information extraorganismal space / lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / cellulose catabolic process / copper ion binding Similarity search - Function | |||||||||
Biological species | Melanocarpus albomyces (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hakulinen, N. / Rouvinen, J. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2006 Title: A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase. Authors: Hakulinen, N. / Kruus, K. / Koivula, A. / Rouvinen, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ih8.cif.gz | 264.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ih8.ent.gz | 209.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ih8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/2ih8 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/2ih8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ih9C 1gw0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61845.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Melanocarpus albomyces (fungus) / Strain: VTT D-96490 / Gene: LAC1 / Production host: Hypocrea jecorina (fungus) / References: UniProt: Q70KY3, laccase |
---|
-Sugars , 5 types, 15 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
---|---|---|---|---|---|---|---|
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 1171 molecules
#7: Chemical | ChemComp-CU / #8: Chemical | #9: Chemical | #10: Chemical | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 17% PEG MME2000, 0.1M Ammonium sulfate, 0.1M Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 21, 2005 |
Radiation | Monochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 88169 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.074 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 11895 / Rsym value: 0.278 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GW0 Resolution: 2→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 11.856 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.264 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.1 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.227 | ||||||||||||||||||||||||||||
Xplor file |
|