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- PDB-7e9x: Trehalase of Arabidopsis thaliana acid mutant -D380A -

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Basic information

Entry
Database: PDB / ID: 7e9x
TitleTrehalase of Arabidopsis thaliana acid mutant -D380A
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: 1.88 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 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 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
C: Trehalase
D: Trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,82812
Polymers260,0914
Non-polymers7378
Water17,258958
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 D380A was also a monomeric protein under nondenaturing conditions.
  • 65.2 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)65,2073
Polymers65,0231
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2073
Polymers65,0231
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2073
Polymers65,0231
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2073
Polymers65,0231
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.657, 129.647, 151.141
Angle α, β, γ (deg.)90.000, 91.027, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 65022.859 Da / Num. of mol.: 4
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) / Strain (production host): BL21(DE3) / References: UniProt: Q9SU50, alpha,alpha-trehalase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 958 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM Tre6P, 0.1 M sodium chloride and 20% PEG3400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→41.55 Å / Num. obs: 169902 / % possible obs: 99.8 % / Redundancy: 6.82 % / Biso Wilson estimate: 28.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.34
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 27135 / CC1/2: 0.838

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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: 1.88→41.55 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5987 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.245 1998 1.18 %
Rwork0.1932 167815 -
obs0.1938 169813 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.37 Å2
Refinement stepCycle: LAST / Resolution: 1.88→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17496 0 48 958 18502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717991
X-RAY DIFFRACTIONf_angle_d0.831924405
X-RAY DIFFRACTIONf_chiral_restr0.04832624
X-RAY DIFFRACTIONf_plane_restr0.00573107
X-RAY DIFFRACTIONf_dihedral_angle_d6.938910655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.39571390.312911672X-RAY DIFFRACTION97.97
1.93-1.980.33051360.290211963X-RAY DIFFRACTION99.91
1.98-2.040.30581430.268912012X-RAY DIFFRACTION99.96
2.04-2.10.27751420.238211996X-RAY DIFFRACTION99.93
2.1-2.180.29911360.223211964X-RAY DIFFRACTION99.96
2.18-2.270.26221440.210511983X-RAY DIFFRACTION99.88
2.27-2.370.26271410.210211999X-RAY DIFFRACTION99.92
2.37-2.50.25391460.209311970X-RAY DIFFRACTION99.98
2.5-2.650.24851460.208312009X-RAY DIFFRACTION99.98
2.65-2.860.22731430.206311985X-RAY DIFFRACTION99.95
2.86-3.140.28161460.206411982X-RAY DIFFRACTION99.91
3.14-3.60.26431420.185712080X-RAY DIFFRACTION99.98
3.6-4.530.20291430.156712040X-RAY DIFFRACTION99.81
4.53-41.550.20311510.156812160X-RAY DIFFRACTION99.83

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