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Yorodumi- PDB-1bug: CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES)-INHIBITOR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bug | ||||||
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Title | CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES)-INHIBITOR COMPLEX WITH PHENYLTHIOUREA (PTU) | ||||||
Components | PROTEIN (CATECHOL OXIDASE) | ||||||
Keywords | OXIDOREDUCTASE / CATECHOL OXIDASE / DICOPPER ENZYME / IPOMOEA BATATAS | ||||||
Function / homology | Function and homology information catechol oxidase / catechol oxidase activity / chloroplast thylakoid lumen / copper ion binding Similarity search - Function | ||||||
Biological species | Ipomoea batatas (sweet potato) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.7 Å | ||||||
Authors | Klabunde, T. / Eicken, C. / Sacchettini, J.C. / Krebs, B. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of a plant catechol oxidase containing a dicopper center. Authors: Klabunde, T. / Eicken, C. / Sacchettini, J.C. / Krebs, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bug.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bug.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1bug ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1bug | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999994, 0.003448, 0.000988), Vector: |
-Components
#1: Protein | Mass: 38814.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COVALENT THIOETHER BOND BETWEEN H109 AND C92 / Source: (natural) Ipomoea batatas (sweet potato) / Organ: MATURE TUBER / References: UniProt: Q9ZP19, catechol oxidase #2: Chemical | ChemComp-CU / #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 51.04 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN AT 277K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0 EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., ...Details: CRYSTALS WERE GROWN AT 277K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0 EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 19405 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.099 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Rsym value: 0.167 / % possible all: 88.9 |
Reflection | *PLUS Num. measured all: 53694 / Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.7→8 Å / σ(F): 3 Details: RESIDUES INVOLVED IN PACKING INTERACTIONS WERE EXCLUDED FROM THE NCS RESTRAINTS.
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Displacement parameters | Biso mean: 13.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev position: 0.0967 Å / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.7 Å2 |