+Open data
-Basic information
Entry | Database: PDB / ID: 1gah | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | GLUCOAMYLASE-471 COMPLEXED WITH ACARBOSE | |||||||||
Components | GLUCOAMYLASE-471 | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION / GLYCOPROTEIN | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Aleshin, A.E. / Stoffer, B. / Firsov, L.M. / Svensson, B. / Honzatko, R.B. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism. Authors: Aleshin, A.E. / Stoffer, B. / Firsov, L.M. / Svensson, B. / 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: 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. #3: Journal: Biochemistry / Year: 1993 Title: Refined Structure for the Complex of 1-Deoxynojirimycin with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4-A Resolution Authors: Harris, E.M. / Aleshin, A.E. / Firsov, L.M. / Honzatko, R.B. #4: Journal: J.Biol.Chem. / Year: 1992 Title: Crystal Structure of Glucoamylase from Aspergillus Awamori Var. X100 to 2.2-A Resolution Authors: Aleshin, A. / Golubev, A. / Firsov, L.M. / Honzatko, R.B. | |||||||||
History |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gah.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gah.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gah_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gah_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1gah_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 1gah_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1gah ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1gah | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Non-polymers , 2 types, 532 molecules A
#1: Protein | Mass: 50551.832 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-471 / Source method: isolated from a natural source / Details: COMPLEXED WITH ACARBOSE / Source: (natural) Aspergillus awamori (mold) / Variant: X100 References: UniProt: P22832, UniProt: P69327*PLUS, glucan 1,4-alpha-glucosidase |
---|---|
#6: Water | ChemComp-HOH / |
-Sugars , 4 types, 13 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 |
---|---|
#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)]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 | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose |
#5: Sugar | ChemComp-MAN / |
-Details
Compound details | GLUCOAMYLASE-471 IS A NATURAL PROTEOLYTIC FRAGMENT OF PARENT GLUCOAMYLASE, WHICH IS INITIALLY ...GLUCOAMYLA |
---|---|
Nonpolymer details | ACARBOSE IS BOUND TO THE ACTIVE SITE OF THE ENZYME. ACARBOSE IS PSEUDOTETRASACCHARIDE. THE LAST TWO ...ACARBOSE IS BOUND TO THE ACTIVE SITE OF THE ENZYME. ACARBOSE IS PSEUDOTETR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4 / Details: pH 4.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop / Details: Golubev, A. M., (1992) J. Mol. Biol., 226, 271. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 34394 / % possible obs: 84.6 % / Observed criterion σ(I): 4 / Redundancy: 2.56 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 5.6 / % possible all: 54.3 |
Reflection | *PLUS % possible obs: 85 % / Num. measured all: 87952 |
Reflection shell | *PLUS Lowest resolution: 2.1 Å / % possible obs: 54 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE GLUCOAMYLASE Resolution: 2→10 Å / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|