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- PDB-7eaw: Trehalase of Arabidopsis thaliana acid mutant -D380A trehalose complex -

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Basic information

Entry
Database: PDB / ID: 7eaw
TitleTrehalase of Arabidopsis thaliana acid mutant -D380A trehalose complex
ComponentsTrehalase
KeywordsHYDROLASE / trehalase / GH37 / Arabidopsis thaliana / Oryza sativa / trehalose / trehalose 6-phosphate / glycoside hydrolase / enzyme kinetics / enzyme structure
Function / homology
Function and homology information


alpha,alpha-trehalase / alpha,alpha-trehalase activity / trehalose catabolic process / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Trehalase / Glycoside hydrolase, family 37 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Lipocalin signature. / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTaguchi, Y. / Saburi, W. / Yu, J. / Imai, R. / Yao, M. / Mori, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18J20503 Japan
CitationJournal: To Be Published
Title: pH-dependent alteration of substrate specificity of plant trehalase and its molecular mechanism
Authors: Taguchi, Y. / Saburi, W. / Yu, J. / Imai, R. / Yao, M. / Mori, H.
History
DepositionMar 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Trehalase
B: Trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0077
Polymers130,0462
Non-polymers9615
Water15,151841
1
A: Trehalase
hetero molecules


  • defined by author
  • Evidence: gel filtration, The wild type enzyme was showed a single band of 63 kDa on SDS-PAGE. This molecular mass was consistent well with estimated values from the amino acid sequence (65 kDa) and ...Evidence: gel filtration, The wild type enzyme was showed a single band of 63 kDa on SDS-PAGE. This molecular mass was consistent well with estimated values from the amino acid sequence (65 kDa) and size exclusion column chromatography (62 kDa), indicating that dNAtTRE1 was also a monomeric protein under nondenaturing conditions.
  • 65.5 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)65,5494
Polymers65,0231
Non-polymers5263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4573
Polymers65,0231
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.671, 104.507, 237.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Trehalase / Alpha / alpha-trehalase / alpha-trehalose glucohydrolase / Trehalase 1 / AtTRE1


Mass: 65022.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A predicted N-terminal transmembrane region (Met1-Leu63) was eliminated.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TRE1, At4g24040, T19F6.15, T19F6.30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SU50, alpha,alpha-trehalase
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM trehalose, 0.1 M sodium fluoride and 20% PEG3400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.16 Å / Num. obs: 122983 / % possible obs: 98.07 % / Redundancy: 9.7 % / Biso Wilson estimate: 21.13 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.45
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 19210 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7e9u

7e9u


Resolution: 1.8→48.16 Å / SU ML: 0.225 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.4343 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2581 2000 1.65 %
Rwork0.228 119493 -
obs0.2285 121493 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8937 0 64 841 9842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729237
X-RAY DIFFRACTIONf_angle_d1.007512540
X-RAY DIFFRACTIONf_chiral_restr0.06341355
X-RAY DIFFRACTIONf_plane_restr0.00551595
X-RAY DIFFRACTIONf_dihedral_angle_d7.32625474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.28641400.24788339X-RAY DIFFRACTION98.17
1.84-1.890.28481410.25288395X-RAY DIFFRACTION98.36
1.89-1.950.31171400.25948429X-RAY DIFFRACTION98.38
1.95-2.010.33051410.27328367X-RAY DIFFRACTION98.52
2.01-2.090.33171400.27968400X-RAY DIFFRACTION98.66
2.09-2.170.32611410.29018431X-RAY DIFFRACTION98.81
2.17-2.270.34381410.28838456X-RAY DIFFRACTION98.9
2.27-2.390.28591430.29248520X-RAY DIFFRACTION99.18
2.39-2.540.2921430.29258498X-RAY DIFFRACTION99.22
2.54-2.730.32321430.28078551X-RAY DIFFRACTION99.27
2.73-3.010.30561430.25528601X-RAY DIFFRACTION99.53
3.01-3.440.2111460.19758657X-RAY DIFFRACTION99.63
3.44-4.340.20971460.16578771X-RAY DIFFRACTION99.88
4.34-48.160.18831520.17019078X-RAY DIFFRACTION99.81

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