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Yorodumi- PDB-2jkx: Galactose oxidase. MatGO. Copper free, expressed in Pichia Pastoris. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jkx | ||||||
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Title | Galactose oxidase. MatGO. Copper free, expressed in Pichia Pastoris. | ||||||
Components | GALACTOSE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / METAL-BINDING / THIOETHER BOND / COPPER / SECRETED / OXIDASES / KELCH REPEAT / COPPER ENZYMES / ENZYME CATALYSIS / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information galactose oxidase / galactose oxidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | GIBBERELLA ZEAE (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Deacon, S.E. / Mahmoud, K. / Spooner, R.K. / Firbank, S.J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J. | ||||||
Citation | Journal: Chembiochem / Year: 2004 Title: Enhanced Fructose Oxidase Activity in a Galactose Oxidase Variant Authors: Deacon, S.E. / Mahmoud, K. / Spooner, R.K. / Firbank, S.J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jkx.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jkx.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/2jkx ftp://data.pdbj.org/pub/pdb/validation_reports/jk/2jkx | HTTPS FTP |
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-Related structure data
Related structure data | 1gogS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 68578.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-680 Source method: isolated from a genetically manipulated source Details: THIOETHER BOND BETWEEN CYS228 AND TYR272 / Source: (gene. exp.) GIBBERELLA ZEAE (fungus) / Plasmid: PPICZALPHAB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33 References: UniProt: Q01745, UniProt: P0CS93*PLUS, galactose oxidase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 18% PEF 8000, 100MM MES PH5.9, 200MM CALCIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→38.3 Å / Num. obs: 53734 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.84→1.9 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.1 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GOG Resolution: 1.84→38.24 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.461 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.13 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→38.24 Å
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Refine LS restraints |
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