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- PDB-1ukp: Crystal structure of soybean beta-amylase mutant substituted at s... -

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Basic information

Entry
Database: PDB / ID: 1ukp
TitleCrystal structure of soybean beta-amylase mutant substituted at surface region
ComponentsBeta-amylase
KeywordsHYDROLASE / (alpha/beta)8 barrel
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKang, Y.N. / Adachi, M. / Mikami, B. / Utsumi, S.
CitationJournal: Protein Eng. / Year: 2003
Title: Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues
Authors: Kang, Y.N. / Adachi, M. / Mikami, B. / Utsumi, S.
History
DepositionAug 31, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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: Beta-amylase
B: Beta-amylase
C: Beta-amylase
D: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,05424
Polymers224,1334
Non-polymers1,92120
Water18,1051005
1
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5136
Polymers56,0331
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5136
Polymers56,0331
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6107
Polymers56,0331
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4175
Polymers56,0331
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.463, 78.801, 88.560
Angle α, β, γ (deg.)89.92, 90.21, 89.90
Int Tables number1
Space group name H-MP1
Detailsthe biological assembly is a monomer

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Components

#1: Protein
Beta-amylase / 1 / 4-alpha-D-glucan maltohydrolase


Mass: 56033.168 Da / Num. of mol.: 4 / Mutation: D374Y / L481R / P487D / K462S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P10538, beta-amylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1005 / 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: 2.24 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
245-50 %ammonium sulfate1reservoir
31 mMEDTA1reservoir
418 mM2-ME1reservoir
50.1 Msodium acetate1reservoirpH5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Apr 17, 2002
RadiationMonochromator: rotating-inclining double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→19.98 Å / Num. all: 335804 / Num. obs: 137751 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 2.44 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.121
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.383 / Num. unique all: 13776 / % possible all: 95.3
Reflection
*PLUS
Num. measured all: 335804
Reflection shell
*PLUS
% possible obs: 95.3 % / Num. unique obs: 13776 / Num. measured obs: 33459

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BYB

1byb


Resolution: 2.1→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1432544.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 11213 10 %RANDOM
Rwork0.2 ---
obs0.2 112238 95.1 %-
all-117984 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.9499 Å2 / ksol: 0.455532 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å21.34 Å22.96 Å2
2--0.72 Å20.22 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15680 0 100 1005 16785
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.82.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 1862 9.9 %
Rwork0.232 16903 -
obs-16903 95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.2345 / Rfactor Rwork: 0.2001
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006334
X-RAY DIFFRACTIONc_angle_deg1.27321
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Lowest resolution: 2.17 Å / Num. reflection Rwork: 11208

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