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- PDB-8z2s: Crystal structure of trehalose synthase mutant R148A from Deinoco... -

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Basic information

Entry
Database: PDB / ID: 8z2s
TitleCrystal structure of trehalose synthase mutant R148A from Deinococcus radiodurans
Componentsmaltose alpha-D-glucosyltransferase
KeywordsISOMERASE / trehalose
Function / homology
Function and homology information


maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsYe, L.C. / Chen, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural and Mutational Analyses of Trehalose Synthase from Deinococcus radiodurans Reveal the Interconversion of Maltose-Trehalose Mechanism.
Authors: Ye, L.C. / Chow, S.Y. / Chang, S.C. / Kuo, C.H. / Wang, Y.L. / Wei, Y.J. / Lee, G.C. / Liaw, S.H. / Chen, W.M. / Chen, S.C.
History
DepositionApr 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: maltose alpha-D-glucosyltransferase
B: maltose alpha-D-glucosyltransferase
C: maltose alpha-D-glucosyltransferase
D: maltose alpha-D-glucosyltransferase
E: maltose alpha-D-glucosyltransferase
F: maltose alpha-D-glucosyltransferase
G: maltose alpha-D-glucosyltransferase
H: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,70632
Polymers519,2148
Non-polymers1,49224
Water23,9961332
1
A: maltose alpha-D-glucosyltransferase
G: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1778
Polymers129,8032
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-33 kcal/mol
Surface area37050 Å2
MethodPISA
2
B: maltose alpha-D-glucosyltransferase
H: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1778
Polymers129,8032
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-46 kcal/mol
Surface area37330 Å2
MethodPISA
3
C: maltose alpha-D-glucosyltransferase
F: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1778
Polymers129,8032
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-45 kcal/mol
Surface area37290 Å2
MethodPISA
4
D: maltose alpha-D-glucosyltransferase
E: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1778
Polymers129,8032
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-46 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.118, 197.475, 134.253
Angle α, β, γ (deg.)90.000, 91.190, 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
maltose alpha-D-glucosyltransferase / Maltose alpha-D-glucosyltransferase


Mass: 64901.727 Da / Num. of mol.: 8 / Mutation: R148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1
Production host: Escherichia coli (E. coli)
References: UniProt: I3NX86, maltose alpha-D-glucosyltransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Tris-HCl pH 8.5, 8% (w/v) polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→20 Å / Num. obs: 204326 / % possible obs: 94.9 % / Redundancy: 3 % / Biso Wilson estimate: 30.53 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.3
Reflection shellResolution: 2.32→2.38 Å / Rmerge(I) obs: 0.179 / Num. unique obs: 180017

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→19.88 Å / SU ML: 0.3082 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 9548 5.04 %
Rwork0.1762 180001 -
obs0.1793 189549 88.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.38 Å2
Refinement stepCycle: LAST / Resolution: 2.32→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35184 0 80 1332 36596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009136304
X-RAY DIFFRACTIONf_angle_d1.06949472
X-RAY DIFFRACTIONf_chiral_restr0.06115112
X-RAY DIFFRACTIONf_plane_restr0.01016544
X-RAY DIFFRACTIONf_dihedral_angle_d6.69914912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.30732140.22184104X-RAY DIFFRACTION60.24
2.35-2.370.34032430.21974382X-RAY DIFFRACTION64.66
2.37-2.40.31551820.20884519X-RAY DIFFRACTION65.53
2.4-2.430.3032560.20754569X-RAY DIFFRACTION67.85
2.43-2.460.30042540.21964703X-RAY DIFFRACTION68.36
2.46-2.50.29562630.21694715X-RAY DIFFRACTION70.15
2.5-2.530.30772450.21264801X-RAY DIFFRACTION70.36
2.53-2.570.30553070.22394867X-RAY DIFFRACTION72.44
2.57-2.610.27532450.22265101X-RAY DIFFRACTION74.99
2.61-2.650.30833290.21875338X-RAY DIFFRACTION78.87
2.65-2.70.30633220.20915716X-RAY DIFFRACTION84.6
2.7-2.750.29863480.20756186X-RAY DIFFRACTION90.5
2.75-2.80.27233070.21196363X-RAY DIFFRACTION93.85
2.8-2.860.28063570.2136558X-RAY DIFFRACTION96.42
2.86-2.920.30123620.21416701X-RAY DIFFRACTION97.93
2.92-2.990.2833660.19476687X-RAY DIFFRACTION98.98
2.99-3.060.28363730.20086715X-RAY DIFFRACTION99.23
3.06-3.150.25853580.19766803X-RAY DIFFRACTION99.31
3.15-3.240.26463390.19776760X-RAY DIFFRACTION99.36
3.24-3.340.2773420.19646784X-RAY DIFFRACTION99.4
3.34-3.460.26513350.18786817X-RAY DIFFRACTION99.32
3.46-3.60.23253430.17726730X-RAY DIFFRACTION98.94
3.6-3.760.23833660.16696756X-RAY DIFFRACTION99.19
3.76-3.960.20263770.15246728X-RAY DIFFRACTION98.94
3.96-4.20.19763680.15076768X-RAY DIFFRACTION98.88
4.2-4.530.18113490.13486742X-RAY DIFFRACTION99.02
4.53-4.970.18343470.13456786X-RAY DIFFRACTION98.82
4.97-5.680.19673190.14286809X-RAY DIFFRACTION99.04
5.68-7.10.20563600.15886773X-RAY DIFFRACTION98.67
7.1-19.880.17043720.14866720X-RAY DIFFRACTION97.28

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