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- PDB-1b1y: SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1b1y
TitleSEVENFOLD MUTANT OF BARLEY BETA-AMYLASE
ComponentsPROTEIN (BETA-AMYLASE)
KeywordsHYDROLASE / HYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / identical protein binding
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-maltose / beta-D-glucopyranose / Beta-amylase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMikami, B. / Yoon, H.J. / Yoshigi, N.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution.
Authors: Mikami, B. / Yoon, H.J. / Yoshigi, N.
#1: Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Construction of a Plasmid Used for the Expression of a Sevenfold-Mutant Barley Beta-Amylase with Increased Thermostability in Escherichia Coli and Properties of the Sevenfold-Mutant Beta-Amylase
Authors: Yoshigi, N. / Okada, Y. / Maeba, H. / Sahara, H. / Tamaki, T.
History
DepositionNov 25, 1998Processing site: RCSB
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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 / 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_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_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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BETA-AMYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8403
Polymers56,3171
Non-polymers5222
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.110, 72.110, 250.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (BETA-AMYLASE)


Mass: 56317.328 Da / Num. of mol.: 1 / Mutation: M185L,S295A,I297V,S350P,S351P,Q352D,A376S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Variant: CV. HARUNA / Plasmid: PB927 / Production host: Escherichia coli (E. coli) / Variant (production host): JM 109 / References: UniProt: P16098, beta-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREF.2 AND REF.3

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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: 2.8 Å3/Da / Density % sol: 57.43 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.1
Details: HUNGING DROP VAPOR DIFFUSION AGAINST 0.1 M PIPES PH 7.1, 0.1 M MGAC2 AND 14% PEG 6000 WITH A PROTEIN CONCENTRATION OF 3 MG/ML., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
250 mMPIPES1drop
30.2 Mmagnesium acetate1drop
47 %PEG60001drop
51 mMPMSF1drop
60.01 %(w/v)1dropNaN3
70.1 MPIPES1reservoir
80.2 Mmagnesium acetate1reservoir
914 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996
RadiationMonochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 22631 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.086
Reflection
*PLUS
Num. measured all: 122221 / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTC
Resolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 -10 %RANDOM
Rwork0.187 ---
obs0.187 18732 79.9 %-
Displacement parametersBiso mean: 31.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å20 Å2
2---2.89 Å20 Å2
3---5.79 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 35 140 4148
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_deg3.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.77
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
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: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.328 119 9.14 %
Rwork0.284 1182 -
obs--45.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM1.CHOTOPH1.CHO
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_deg24.77
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.22

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