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Yorodumi- PDB-3gly: REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMO... -
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-Basic information
Entry | Database: PDB / ID: 3gly | ||||||||||||
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Title | REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100 | ||||||||||||
Components | GLUCOAMYLASE-471 | ||||||||||||
Keywords | HYDROLASE | ||||||||||||
Function / homology | Function and homology information glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / starch binding / polysaccharide catabolic process Similarity search - Function | ||||||||||||
Biological species | Aspergillus awamori (mold) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||||||||
Authors | Aleshin, A.E. / Hoffman, C. / Firsov, L.M. / Honzatko, R.B. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Refined crystal structures of glucoamylase from Aspergillus awamori var. X100. Authors: Aleshin, A.E. / Hoffman, C. / Firsov, L.M. / Honzatko, R.B. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Refined Structure for the Complex of Acarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4 Angstroms Resolution Authors: Aleshin, A.E. / Firsov, L.M. / Honzatko, R.B. #2: Journal: Biochemistry / Year: 1993 Title: Refined Structure of the Complex of 1-Deoxynojirimycin with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4 Angstroms Resolution Authors: Harris, E.M.S. / Aleshin, A.E. / Firsov, L.M. / Honzatko, R.B. #3: Journal: J.Biol.Chem. / Year: 1992 Title: Crystal Structure of Glucoamylase from Aspergillus Awamori Var. X100 to 2.2 Angstroms Resolution Authors: Aleshin, A.E. / Golubev, A. / Firsov, L.M. / Honzatko, R.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gly.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gly.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/3gly ftp://data.pdbj.org/pub/pdb/validation_reports/gl/3gly | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: GLY 23 - ALA 24 OMEGA = 0.50 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO 46 / 3: CIS PROLINE - PRO 123 4: RESIDUES ASN 171 AND ASN 395 ARE SITES OF N-GLYCOSYLATION. 5: RESIDUES SER 443, SER 444, THR 452, SER 453, SER 455, THR 457, SER 459, SER 460, THR 462 AND THR 464 ARE SITES OF O-GLYCOSYLATION. |
-Components
#1: Protein | Mass: 50450.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus awamori (mold) References: UniProt: P22832, UniProt: P69327*PLUS, glucan 1,4-alpha-glucosidase | ||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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 | ||||
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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: Sugar | ChemComp-MAN / #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.95 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. all: 35431 / Num. obs: 33871 / Observed criterion σ(F): 2 / Num. measured all: 233315 / Rmerge(I) obs: 0.044 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.141 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |