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Yorodumi- PDB-1al7: THREE-DIMENSIONAL STRUCTURES OF GLYCOLATE OXIDASE WITH BOUND ACTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1al7 | ||||||
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Title | THREE-DIMENSIONAL STRUCTURES OF GLYCOLATE OXIDASE WITH BOUND ACTIVE-SITE INHIBITORS | ||||||
Components | GLYCOLATE OXIDASEHydroxyacid oxidase (glycolate oxidase) 1 | ||||||
Keywords | FLAVOPROTEIN / DRUG DESIGN / INHIBITOR BINDING | ||||||
Function / homology | Function and homology information oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / response to other organism / peroxisome / FMN binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.6 Å | ||||||
Authors | Stenberg, K. / Lindqvist, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: Three-dimensional structures of glycolate oxidase with bound active-site inhibitors. Authors: Stenberg, K. / Lindqvist, Y. #1: Journal: Protein Expr.Purif. / Year: 1996 Title: High-Level Expression, Purification, and Crystallization of Recombinant Spinach Glycolate Oxidase in Escherichia Coli Authors: Stenberg, K. / Lindqvist, Y. #2: Journal: J.Mol.Biol. / Year: 1989 Title: Refined Structure of Spinach Glycolate Oxidase at 2 A Resolution Authors: Lindqvist, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1al7.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1al7.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1al7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1al7 ftp://data.pdbj.org/pub/pdb/validation_reports/al/1al7 | 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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-Components
#1: Protein | Mass: 39336.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GLYCOLATE OXIDASE COMPLEXED WITH FMN AND AN INHIBITOR Source: (gene. exp.) Spinacia oleracea (spinach) / Cell line: BL21 / Cellular location: PEROXISOME / Plasmid: PKS20+ / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P05414, (S)-2-hydroxy-acid oxidase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-HST / |
#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: 4.76 Å3/Da / Density % sol: 74.13 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.3 Details: PROTEIN WAS CRYSTALLISED FROM 50MM TRIS-BUFFER PH 8.3, 0.25 MG/ML FMN, 4% TERTIARY BUTANOL, SATURATED WITH THE INHIBITOR. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 20291 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.99 |
Reflection shell | Resolution: 2.6→2.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.206 / % possible all: 74.4 |
Reflection | *PLUS Num. measured all: 48698 |
Reflection shell | *PLUS % possible obs: 74.4 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.6→8 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Details: TOPOLOGY AND PARAMETER FILES FOR THE TKCA-INHIBITOR WERE CREATED USING THE PROGRAMME XPLO2D (REF: [O/X-PLOR DICTIONARIES] G.J. KLEYWEGT, DICTIONARIES FOR HETEROS, ESF/CCP4 NEWSLETTER 31,JUNE ...Details: TOPOLOGY AND PARAMETER FILES FOR THE TKCA-INHIBITOR WERE CREATED USING THE PROGRAMME XPLO2D (REF: [O/X-PLOR DICTIONARIES] G.J. KLEYWEGT, DICTIONARIES FOR HETEROS, ESF/CCP4 NEWSLETTER 31,JUNE 1995, PP. 45-50). BOND LENGTHS AND ANGLES ARE FROM IDEALIZED STRUCTURES.
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Displacement parameters | Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.76 Å / Total num. of bins used: 12 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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