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- PDB-2dqx: mutant beta-amylase (W55R) from soy bean -

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Basic information

Entry
Database: PDB / ID: 2dqx
Titlemutant beta-amylase (W55R) from soy bean
ComponentsBeta-amylase
KeywordsHYDROLASE / amylase mutant sliding soy bean
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: 2.2 Å
AuthorsIshikawa, K.
CitationJournal: Biochemistry / Year: 2007
Title: Kinetic and structural analysis of enzyme sliding on a substrate: multiple attack in beta-amylase
Authors: Ishikawa, K. / Nakatani, H. / Katsuya, Y. / Fukazawa, C.
History
DepositionJun 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Beta-amylase


Theoretical massNumber of molelcules
Total (without water)55,9701
Polymers55,9701
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.042, 85.042, 145.083
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: 55970.172 Da / Num. of mol.: 1 / Mutation: W55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pBAMSO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q42795, beta-amylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M sodium acetate (pH 5.4), 1mM EDTA, 50% ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.835 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.835 Å / Relative weight: 1
ReflectionResolution: 2.2→19.95 Å / Num. obs: 31087 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.074
Reflection shellHighest resolution: 2.2 Å / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDP

1wdp


Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2526968.69 / 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
Rfree0.252 1513 4.9 %RANDOM
Rwork0.206 ---
obs0.206 30579 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.5074 Å2 / ksol: 0.406937 e/Å3
Displacement parametersBiso mean: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20.08 Å20 Å2
2--2.23 Å20 Å2
3----4.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 0 327 4248
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_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 250 5.2 %
Rwork0.221 4578 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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