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Yorodumi- PDB-1agm: Refined structure for the complex of acarbose with glucoamylase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1agm | |||||||||
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Title | Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution | |||||||||
Components | GLUCOAMYLASE-471 | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / starch binding / fungal-type vacuole / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Aspergillus awamori (mold) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | |||||||||
Authors | Aleshin, A.E. / Firsov, L.M. / Honzatko, R.B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution. Authors: Aleshin, A.E. / Firsov, L.M. / Honzatko, R.B. #1: 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. #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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Remark 650 | HELIX THE POLYPEPTIDE CHAIN FOLDS INTO AN ALPHA/ALPHA-BARREL, COMPRISING 12 HELICES. | |||||||||
Remark 700 | SHEET MOST OF THE SHEETS FOR GLUCOAMYLASE-471 ARE HAIRPIN LOOPS THAT CONNECT HELICES. THESE LOOPS ...SHEET MOST OF THE SHEETS FOR GLUCOAMYLASE-471 ARE HAIRPIN LOOPS THAT CONNECT HELICES. THESE LOOPS HAVE TWO OR MORE H-BONDS BETWEEN THE ANTIPARALLEL STRANDS THAT COMPRISE THEM. IN ADDITION INDIVIDUAL LOOPS PACK TOGETHER, BUT THERE EXISTS GENERALLY ONLY ONE H-BOND BETWEEN A LOOP AND ITS NEIGHBOR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1agm.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1agm.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 1agm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1agm_validation.pdf.gz | 689.4 KB | Display | wwPDB validaton report |
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Full document | 1agm_full_validation.pdf.gz | 701.6 KB | Display | |
Data in XML | 1agm_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1agm_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agm ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agm | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Atom site foot note | 1: RESIDUES GLY 23 AND ALA 24 FORM A CIS PEPTIDE. / 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
-Protein / Non-polymers , 2 types, 536 molecules A
#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: P23176, UniProt: P69327*PLUS, glucan 1,4-alpha-glucosidase |
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#6: Water | ChemComp-HOH / |
-Sugars , 4 types, 14 molecules
#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 | ||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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: Polysaccharide | #5: Sugar | ChemComp-MAN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.64 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.95 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 2.3 Å / Num. all: 26797 / Num. obs: 21212 / Num. measured all: 51528 / Rmerge(I) obs: 0.032 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.124 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |