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- PDB-1glm: REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMO... -

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Basic information

Entry
Database: PDB / ID: 1glm
TitleREFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100
ComponentsGLUCOAMYLASE-471
KeywordsHYDROLASE
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
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
alpha-D-mannopyranose / Glucoamylase
Similarity search - Component
Biological speciesAspergillus awamori (mold)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsAleshin, 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: To be Published
Title: Refined Structure for the Complex of Acarbose with Glucoamylase from Aspergillus Awamori Var. X100 to 2.4A 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
Authors: Aleshin, A.E. / Golubev, A. / Firsov, L.M. / Honzatko, R.B.
History
DepositionApr 25, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.PDB_ins_code / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOAMYLASE-471
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,56013
Polymers50,4511
Non-polymers4,11012
Water10,106561
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.800, 104.400, 48.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: GLY 23 - ALA 24 OMEGA = 1.53 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.

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Components

#1: Protein GLUCOAMYLASE-471


Mass: 50450.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus awamori (mold) / References: UniProt: P69327, glucan 1,4-alpha-glucosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-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
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE NUMBER 102 IS SKIPPED SO THAT THE NUMBERING OF THE RESIDUES IS CONSISTENT WITH GLUCOAMYLASE ...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 ASPARGILLUS AWAMORI VAR. KAWACHI. THE RESULTING SEQUENCE DIFFERS FROM THE ASPERGILLUS NIGER SEQUENCE (PIR REFERENCE ALASG4) AT THE FOLLOWING POSITION: PIR RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ LEU 84 ILE 60

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal grow
*PLUS
pH: 5.95 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMpotassium phosphate1drop
313 %(w/v)PEG60001drop
450 mMphosphate1reservoir
530 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. all: 24005 / Num. obs: 20905 / Num. measured all: 57478 / Rmerge(I) obs: 0.035

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.122 20407
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 265 561 4388
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0280.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.591
X-RAY DIFFRACTIONp_mcangle_it1.0041.5
X-RAY DIFFRACTIONp_scbond_it1.8422
X-RAY DIFFRACTIONp_scangle_it2.7813
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1380.15
X-RAY DIFFRACTIONp_singtor_nbd0.2220.25
X-RAY DIFFRACTIONp_multtor_nbd0.1520.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1820.25
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor28.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.122
Solvent computation
*PLUS
Displacement parameters
*PLUS

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