[English] 日本語
Yorodumi- PDB-1gw0: Crystal Structure of Laccase from Melanocarpus albomyces in Four ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gw0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Laccase from Melanocarpus albomyces in Four Copper Form | |||||||||
Components | LACCASE-1 | |||||||||
Keywords | OXIDOREDUCTASE / LACCASE / MULTI-COPPER OXIDASES / OXYGEN REDUCTION / ASCOMYCETE / C-TERMINAL PLUG | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Hakulinen, N. / Kiiskinen, L.-L. / Kruus, K. / Saloheimo, M. / Koivula, A. / Rouvinen, J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Crystal Structure of a Laccase from Melanocarpus Albomyces with an Intact Trinuclear Copper Site Authors: Hakulinen, N. / Kiiskinen, L.-L. / Kruus, K. / Saloheimo, M. / Paananen, A. / Koivula, A. / Rouvinen, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gw0.cif.gz | 259.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gw0.ent.gz | 207.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/1gw0 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/1gw0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1a65S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, -0.0003, 0.0031), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61845.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MELANOCARPUS ALBOMYCES (fungus) / References: UniProt: Q70KY3, laccase |
---|
-Sugars , 6 types, 15 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 | ||||||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #10: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 810 molecules
#7: Chemical | #8: Chemical | ChemComp-CU / #9: Chemical | #11: Chemical | #12: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
---|---|
Crystal grow | pH: 4.2 Details: 25% PMME 2000, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.2 |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 15, 2001 / Details: OSMIC CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 49561 / % possible obs: 95 % / Redundancy: 1.9 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.28 / % possible all: 86.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A65 Resolution: 2.4→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|