[English] 日本語
Yorodumi
- PDB-1gai: GLUCOAMYLASE-471 COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gai
TitleGLUCOAMYLASE-471 COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE
ComponentsGLUCOAMYLASE-471
KeywordsHYDROLASE / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION / GLYCOPROTEIN
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
Glucoamylase, starch-binding / Glucoamylase, CBM20 domain / Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. ...Glucoamylase, starch-binding / Glucoamylase, CBM20 domain / Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
dihydro-alpha-acarbose / alpha-D-mannopyranose / Glucoamylase / Glucoamylase
Similarity search - Component
Biological speciesAspergillus awamori (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAleshin, 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: FEBS Lett. / Year: 1995
Title: Refined Structure for the Complex of D-Gluco-Dihydroacarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.2 A Resolution: Dual Conformations for Extended Inhibitors Bound to the ...Title: Refined Structure for the Complex of D-Gluco-Dihydroacarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.2 A Resolution: Dual Conformations for Extended Inhibitors Bound to the Active Site of Glucoamylase
Authors: Stoffer, B. / Aleshin, A.E. / Firsov, L.M. / Svensson, B. / Honzatko, R.B.
#2: 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.
#3: 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.
#4: 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.
#5: 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
DepositionMar 6, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOAMYLASE-471
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,52814
Polymers50,6091
Non-polymers4,91913
Water9,926551
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.900, 104.400, 48.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Non-polymers , 2 types, 552 molecules A

#1: Protein GLUCOAMYLASE-471 / GLUCOAMYLASE-II / GLUCAN 1 / 4-ALPHA-GLUCOSIDASE


Mass: 50608.883 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-471 / Source method: isolated from a natural source / Details: COMPLEXED WITH D-GLUCO-DIHYDROACARBOSE / Source: (natural) Aspergillus awamori (mold) / Variant: X100
References: UniProt: P22832, UniProt: P69327*PLUS, glucan 1,4-alpha-glucosidase
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O

-
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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / dihydro-alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 647.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: dihydro-alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RC^RCO/7C$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Compound detailsGLUCOAMYLASE-471 IS A NATURAL PROTEOLYTIC FRAGMENT OF PARENT GLUCOAMYLASE, WHICH IS INITIALLY ...GLUCOAMYLASE-471 IS A NATURAL PROTEOLYTIC FRAGMENT OF PARENT GLUCOAMYLASE, WHICH IS INITIALLY SECRETED BY FUNGI. GLUCOAMYLASE-471 LACKS THE STARCH-BINDING DOMAIN AND A PART OF THE O-GLYCOSYLATED LINKER DOMAIN. THE ACTUAL LENGTH OF GLUCOAMYLASE-471 FROM ASPERGILLUS AWAMORI VAR. X100 IS NOT DETERMINED EXACTLY. THE CRYSTALLOGRAPHICALLY OBSERVED LENGTH VARIES BETWEEN 471 AND 473 RESIDUES. THE SEQUENCE USED IS THAT OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. KAWACHI (SEE JRNL AND REFERENCE 4). RESIDUE NUMBERS ARE DISCONTINUOUS. RESIDUE NUMBER 102 IS SKIPPED SO THAT THE NUMBERING OF THE RESIDUES IS CONSISTENT WITH GLUCOAMYLASE FROM ASPERGILLUS NIGER. RESIDUE NUMBERS 141, 240, 319, 320, AND 445 HAVE THE AMINO ACID TYPE CORRESPONDING TO THE GLUCOAMYLASE FROM ASPERGILLUS NIGER, RATHER THAN THAT OF ASPERGILLUS AWAMORI VAR. KAWACHI. THE POLYPEPTIDE CHAIN FOLDS INTO AN ALPHA/ALPHA-BARREL, COMPRISING 12 HELICES.
Nonpolymer detailsD-GLUCO-DIHYDROACARBOSE IS BOUND TO THE ACTIVE SITE OF THE ENZYME. D-GLUCO-DIHYDROACARBOSE IS A ...D-GLUCO-DIHYDROACARBOSE IS BOUND TO THE ACTIVE SITE OF THE ENZYME. D-GLUCO-DIHYDROACARBOSE IS A PSEUDOTETRASACCHARIDE. THE LAST TWO RESIDUES OF THE REDUCING END ARE PRESENT IN TWO ALTERNATE CONFORMATIONS, ONE OF WHICH (OCCUPANCY 0.37) CORRESPONDS TO THE CONFORMATION OF ACARBOSE OBSERVED AT PH 6.0. SEE RELATED PROTEIN DATA BANK ENTRY 1AGM OF THE STRUCTURE OF GLUCOAMYLASE-471 COMPLEXED WITH ACARBOSE DETERMINED AT PH 6.0 SEE RELATED PROTEIN DATA BANK ENTRY 1GAH FOR THE STRUCTURE OF GLUCOAMYLASE-741 COMPLEXED WITH ACARBOSE DETERMINED AT PH 4.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growpH: 4 / Details: pH 4.
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
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
230 %(w/v)PEG60001drop
30.15 Msodium phosphate1drop
430 %(w/v)PEG60001reservoir
50.15 Msodium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 20, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. obs: 64147 / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 4.66 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.16
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.3 / % possible all: 75.5
Reflection
*PLUS
Num. obs: 64713 / Num. measured all: 298712
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 75 %

-
Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE GLOCOAMYLASE

Resolution: 1.7→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.167 -5 %
Rwork0.147 --
obs0.147 61302 93.4 %
Displacement parametersBiso mean: 14.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 320 551 4444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARH3.CHOTOPH3.CHO
X-RAY DIFFRACTION2GLUCOACR_SUGARS_XPLOR.PARGLUCOACR_SUGARS_XPLOR.TOP
X-RAY DIFFRACTION3GLUCOACR_VLN.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more