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Yorodumi- PDB-1ayx: CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ayx | ||||||
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Title | CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS | ||||||
Components | GLUCOAMYLASE | ||||||
Keywords | HYDROLASE / GLUCOAMYLASE / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION | ||||||
Function / homology | Function and homology information glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / fungal-type vacuole / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Saccharomycopsis fibuligera (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Sevcik, J. / Hostinova, E. / Gasperik, J. / Solovicova, A. / Wilson, K.S. / Dauter, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of glucoamylase from Saccharomycopsis fibuligera at 1.7 A resolution. Authors: Sevcik, J. / Solovicova, A. / Hostinova, E. / Gasperik, J. / Wilson, K.S. / Dauter, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ayx.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayx.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ayx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ayx_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 1ayx_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 1ayx_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 1ayx_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayx ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54659.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomycopsis fibuligera (fungus) / Gene: GLU1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08017, glucan 1,4-alpha-glucosidase |
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#2: Chemical | ChemComp-TRS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.1 Details: 50 MM ACETATE BUFFER, PH 5.1, 15 % (W/V) PEG 8000 HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 4.7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 17.8 Å2 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 29 Å / Num. obs: 56654 / % possible obs: 99.4 % / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.71 Å / Mean I/σ(I) obs: 3.5 |
-Processing
Software | Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→30 Å / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 19.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 0.149 / Rfactor obs: 0.144 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.181 / Num. reflection Rfree: 1157 / % reflection Rfree: 2 % / Rfactor all: 0.149 / Rfactor obs: 0.144 |