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- PDB-1bfn: BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bfn
TitleBETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX
ComponentsBETA-AMYLASE
KeywordsHYDROLASE / BETA-AMYLASE / BETA-CYCLODEXTRIN / RECOMBINANT
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cyclodextrin / Beta-amylase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 2.07 Å
AuthorsAdachi, M. / Mikami, B. / Katsube, T. / Utsumi, S.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.
Authors: Adachi, M. / Mikami, B. / Katsube, T. / Utsumi, S.
#1: Journal: Biochemistry / Year: 1994
Title: Crystal Structures of Soybean Beta-Amylase Reacted with Beta-Maltose and Maltal: Active Site Components and Their Apparent Roles in Catalysis
Authors: Mikami, B. / Degano, M. / Hehre, E.J. / Sacchettini, J.C.
#2: 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.
History
DepositionMay 22, 1998Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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 / _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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: BETA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2143
Polymers55,9651
Non-polymers1,2492
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.030, 86.030, 144.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein BETA-AMYLASE /


Mass: 55965.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P10538, beta-amylase
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin / Cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 277 K / pH: 5.4
Details: 49% (NH4)2SO4, 0.1M NAOAC PH 5.4, 18MM 2-MERCAPTOETHANOL, AT 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
224.5 %ammonium sulfate1drop
30.05 Msodium acetate1drop
40.5 mMEDTA1drop
59 mMME1drop
649 %ammonium sulfate1reservoir
70.1 Msodium acetate1reservoir
81 mMEDTA1reservoir
918 mM1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å
Reflection
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 10 Å / Num. all: 39214 / Num. obs: 36696 / Observed criterion σ(I): 2 / Num. measured all: 152726 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.07→10 Å / Data cutoff low absF: 1 / Cross valid method: POSTERIORI / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3402 10 %RANDOM
Rwork0.158 ---
obs0.158 34127 80.7 %-
Displacement parametersBiso mean: 22.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.07→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 82 318 4315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
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
LS refinement shellResolution: 2.07→2.16 Å
RfactorNum. reflection% reflection
Rfree0.248 360 6.74 %
Rwork0.218 3163 -
obs--75.1 %
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_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

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