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- PDB-1agm: Refined structure for the complex of acarbose with glucoamylase f... -

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Entry
Database: PDB / ID: 1agm
TitleRefined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution
ComponentsGLUCOAMYLASE-471
KeywordsHYDROLASE
Function / homologySix-hairpin glycosidase-like superfamily / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Glucoamylase active site region signature. / Glucoamylase / Carbohydrate binding module family 20 / Glucoamylase, starch-binding / Six-hairpin glycosidase superfamily / GH15-like domain / Glycosyl hydrolases family 15 ...Six-hairpin glycosidase-like superfamily / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Glucoamylase active site region signature. / Glucoamylase / Carbohydrate binding module family 20 / Glucoamylase, starch-binding / Six-hairpin glycosidase superfamily / GH15-like domain / Glycosyl hydrolases family 15 / Immunoglobulin-like fold / Carbohydrate-binding-like fold / Glucoamylase, CBM20 domain / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / starch binding / polysaccharide catabolic process / Glucoamylase I / Glucoamylase
Function and homology information
Specimen sourceAspergillus awamori (mold)
MethodX-RAY DIFFRACTION / 2.3 Å resolution
AuthorsAleshin, 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 13, 1994 / Release: Sep 30, 1994
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 30, 1994Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site
Remark 650HELIX THE POLYPEPTIDE CHAIN FOLDS INTO AN ALPHA/ALPHA-BARREL, COMPRISING 12 HELICES.
Remark 700SHEET 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOAMYLASE-471
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,05026
Polyers50,4511
Non-polymers5,59925
Water9,638535
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)116.700, 103.900, 48.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21
Atom site foot note1: 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.

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide GLUCOAMYLASE-471


Mass: 50450.730 Da / Num. of mol.: 1 / Source: (gene. exp.) Aspergillus awamori (mold) / Genus: Aspergillus
References: UniProt: P23176, UniProt: P69327*PLUS, glucan 1,4-alpha-glucosidase

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Non-polymers , 5 types, 560 molecules

#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 2 / Formula: C6H12O6
#4: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 17 / Formula: C6H12O6
#5: Chemical ChemComp-ACR / ALPHA-ACARBOSE / 1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE


Mass: 645.605 Da / Num. of mol.: 2 / Formula: C25H43NO18
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 / Density percent sol: 57.64 %
Crystal grow
*PLUS
pH: 5.95 / Method: vapor diffusion
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
115 mg/mlprotein1drop
250 mMpotassium phosphate1drop
313 %(w/v)PEG60001drop
450 mMphosphate1reservoir
520-30 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.3 Å / Number obs: 21212 / Number all: 26797 / Number measured all: 51528 / Rmerge I obs: 0.032

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefineSigma F: 1
Least-squares processR factor obs: 0.124 / Highest resolution: 2.3 Å / Lowest resolution: 1 Å / Number reflection obs: 20601
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 3562 / Nucleic acid: 0 / Ligand: 353 / Solvent: 535 / Total: 4450
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.020
X-RAY DIFFRACTIONp_angle_d0.0290.300
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6431.000
X-RAY DIFFRACTIONp_mcangle_it1.0001.500
X-RAY DIFFRACTIONp_scbond_it1.9722.000
X-RAY DIFFRACTIONp_scangle_it2.8643.000
X-RAY DIFFRACTIONp_plane_restr0.0120.020
X-RAY DIFFRACTIONp_chiral_restr0.1370.150
X-RAY DIFFRACTIONp_singtor_nbd0.2240.250
X-RAY DIFFRACTIONp_multtor_nbd0.1530.250
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1920.250
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.303.00
X-RAY DIFFRACTIONp_staggered_tor13.8015.00
X-RAY DIFFRACTIONp_orthonormal_tor28.7020.00
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.124

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