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- PDB-1bya: CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALT... -

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Basic information

Entry
Database: PDB / ID: 1bya
TitleCRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS
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
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMikami, B. / Degano, M. / Hehre, E.J. / Sacchettini, J.C.
Citation
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.
#1: Journal: Biochemistry / Year: 1993
Title: The 2.0-Angstroms 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
DepositionJan 25, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)56,1672
Polymers56,0711
Non-polymers961
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.200, 86.200, 144.200
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
2: LEU 419 - ARG 420 OMEGA = 16.21 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein BETA-AMYLASE


Mass: 56071.316 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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal grow
*PLUS
Method: unknown / Details: Morita, Y., (1975) J. Biochem., 77, 343.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1140 mg/mlprotein11
250 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 45035 / Num. measured all: 219183

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→9 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.169 -
obs0.169 45035
Refinement stepCycle: LAST / Resolution: 2.2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 5 320 4254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.403
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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

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