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- PDB-1btc: THREE-DIMENSIONAL STRUCTURE OF SOYBEAN BETA-AMYLASE DETERMINED AT... -

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Basic information

Entry
Database: PDB / ID: 1btc
TitleTHREE-DIMENSIONAL STRUCTURE OF SOYBEAN BETA-AMYLASE DETERMINED AT 3.0 ANGSTROMS RESOLUTION: PRELIMINARY CHAIN TRACING OF THE COMPLEX WITH ALPHA-CYCLODEXTRIN
ComponentsBETA-AMYLASE
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Beta-amylase active site 2. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-cyclodextrin / BETA-MERCAPTOETHANOL / Beta-amylase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMikami, B. / Hehre, E.J. / Sato, M. / Katsube, Y. / Hirose, M. / Morita, Y. / Sacchettini, J.C.
Citation
Journal: Biochemistry / Year: 1993
Title: The 2.0-A resolution structure of soybean beta-amylase complexed with alpha-cyclodextrin.
Authors: Mikami, B. / Hehre, E.J. / Sato, M. / Katsube, Y. / Hirose, M. / Morita, Y. / Sacchettini, J.C.
#1: Journal: J.Biochem.(Tokyo) / Year: 1992
Title: Three-dimensional structure of soybean beta-amylase determined at 3.0 A resolution: preliminary chain tracing of the complex with alpha-cyclodextrin.
Authors: Mikami, B. / Sato, M. / Shibata, T. / Hirose, M. / Aibara, S. / Katsube, Y. / Morita, Y.
#2: Journal: Denpun Kagaku / Year: 1991
Title: X-Ray Crystal Structure of Soybean Beta-Amylase
Authors: Mikami, B. / Shibata, T. / Hirose, M. / Aibara, S. / Sato, M. / Katsube, Y. / Morita, Y.
#3: Journal: J.Biochem.(Tokyo) / Year: 1975
Title: Crystallization and Preliminary X-Ray Investigation of Soybean Beta-Amylase
Authors: Morita, Y. / Aibara, S. / Yamashita, H. / Yagi, F. / Suganuma, T. / Hiromi, K.
History
DepositionFeb 18, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 2.1Mar 26, 2025Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0967
Polymers55,6971
Non-polymers1,3996
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.100, 86.100, 144.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO 201

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Components

#1: Protein BETA-AMYLASE


Mass: 55696.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / References: UniProt: P10538, beta-amylase
#2: Polysaccharide Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: alpha-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,6,6/[a2122h-1a_1-5]/1-1-1-1-1-1/a1-f4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Macetate12
250 %satammonium sulphate12
30.1 M12NaCl
418 mM2-mercaptoethanol12
51 mMEDTA12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 15187 / Num. measured all: 20136 / Rmerge(I) obs: 0.037

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→9 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.177 -
obs0.177 30045
Refinement stepCycle: LAST / Resolution: 2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 87 318 4334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 9 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.08
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_plane_restr1.16

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