+Open data
-Basic information
Entry | Database: PDB / ID: 3pxl | |||||||||
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Title | Type-2 Cu-depleted fungus laccase from Trametes hirsuta | |||||||||
Components | Laccase | |||||||||
Keywords | OXIDOREDUCTASE / 4-copper protein / metal-binding / type-2 Cu-depleted | |||||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Trametes hirsuta (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Polyakov, K.M. / Fedorova, T.V. / Kurzeev, S.A. / Popov, A.N. / Lamzin, V.S. / Koroleva, O.V. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of T2-depleted fungal laccase from Trametes hirsuta at low and high dose of ionization radiation. Authors: Polyakov, K.M. / Fedorova, T.V. / Kurzeev, S.A. / Popov, A.N. / Lamzin, V.S. / Koroleva, O.V. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of native laccase from Trametes hirsuta at 1.8 A resolution Authors: Polyakov, K.M. / Fedorova, T.V. / Stepanova, E.V. / Cherkashin, E.A. / Kurzeev, S.A. / Storokopytov, B.V. / Lamzin, V.S. / Koroleva, O.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pxl.cif.gz | 384.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pxl.ent.gz | 312.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/3pxl ftp://data.pdbj.org/pub/pdb/validation_reports/px/3pxl | HTTPS FTP |
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-Related structure data
Related structure data | 3fpxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53632.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trametes hirsuta (fungus) / References: UniProt: B2L9C1, laccase |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-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 |
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#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 | 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 , 2 types, 643 molecules
#5: Chemical | ChemComp-CU / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein solution 44 mg/ml in 0.02M potassium phosphate, pH 6.0. Reservoir solution is 30% PEG 1500, 0.02M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8156 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8156 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→60 Å / Num. all: 160653 / Num. obs: 155833 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.081 |
Reflection shell | Resolution: 1.2→60 Å / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FPX Resolution: 1.2→60 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.397 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.361 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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