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- PDB-1ac0: GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN COMPLEX WITH CYCLODE... -

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Basic information

Entry
Database: PDB / ID: 1ac0
TitleGLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN COMPLEX WITH CYCLODEXTRIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsGLUCOAMYLASE
KeywordsHYDROLASE / STARCH BINDING DOMAIN
Function / homology
Function and homology information


polysaccharide metabolic process / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / starch binding / polysaccharide catabolic process / endoplasmic reticulum
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 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cyclodextrin / Glucoamylase / Glucoamylase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsSorimachi, K. / Le Gal-Coeffet, M.-F. / Williamson, G. / Archer, D.B. / Williamson, M.P.
Citation
Journal: Structure / Year: 1997
Title: Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
Authors: Sorimachi, K. / Le Gal-Coeffet, M.F. / Williamson, G. / Archer, D.B. / Williamson, M.P.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Solution Structure of the Granular Starch Binding Domain of Glucoamylase from Aspergillus Niger by Nuclear Magnetic Resonance Spectroscopy
Authors: Sorimachi, K. / Jacks, A.J. / Le Gal-Coeffet, M.F. / Williamson, G. / Archer, D.B. / Williamson, M.P.
History
DepositionFeb 10, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / 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_nmr_refine / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_nmr_refine.details / _pdbx_nmr_software.version / _pdbx_validate_close_contact.PDB_ins_code_2 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOAMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1913
Polymers11,8851
Non-polymers2,3062
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4160 Å2
ΔGint39 kcal/mol
Surface area5820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100RANDOM FROM 81 GOOD STRUCTURES
Representative

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Components

#1: Protein GLUCOAMYLASE / 1 / 4-ALPHA-D-GLUCAN GLUCOHYDROLASE


Mass: 11884.820 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN, RESIDUES 509 - 616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: AB4.1 / Plasmid: PIGF / Gene (production host): A. NIGER GLAA / Production host: Aspergillus niger (mold)
References: UniProt: P04064, UniProt: P69328*PLUS, glucan 1,4-alpha-glucosidase
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED TOCSY
121NOESY

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Sample preparation

Sample conditionspH: 5.7 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 500 / Manufacturer: Bruker / Model: AMX 500 / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE VALUES SHOWN IN THE TEMPERATURE FACTOR FIELD ARE ATOMIC RMSD VALUES OF 41 STRUCTURES TO THE UNMINIMIZED AVERAGE STRUCTURE.
NMR ensembleConformer selection criteria: RANDOM FROM 81 GOOD STRUCTURES
Conformers calculated total number: 100 / Conformers submitted total number: 1

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