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- PDB-8ywd: Crystal structure of trehalose synthase mutant N253C from Deinoco... -

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Basic information

Entry
Database: PDB / ID: 8ywd
TitleCrystal structure of trehalose synthase mutant N253C 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: 2.65 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
DepositionMar 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 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)521,30732
Polymers519,8158
Non-polymers1,49224
Water1,964109
1
A: maltose alpha-D-glucosyltransferase
E: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3278
Polymers129,9542
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-46 kcal/mol
Surface area37480 Å2
MethodPISA
2
B: maltose alpha-D-glucosyltransferase
D: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3278
Polymers129,9542
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area37650 Å2
MethodPISA
3
C: maltose alpha-D-glucosyltransferase
H: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3278
Polymers129,9542
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-34 kcal/mol
Surface area37600 Å2
MethodPISA
4
F: maltose alpha-D-glucosyltransferase
G: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3278
Polymers129,9542
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-35 kcal/mol
Surface area37290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.321, 196.852, 131.188
Angle α, β, γ (deg.)90.000, 93.070, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
maltose alpha-D-glucosyltransferase / Maltose alpha-D-glucosyltransferase


Mass: 64976.883 Da / Num. of mol.: 8 / Mutation: N253C,R97W, T313I, I380V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_2036 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RST7, 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.: 109 / 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: 2.65→30 Å / Num. obs: 137854 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 42.99 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.5
Reflection shellResolution: 2.65→2.74 Å / Num. unique obs: 43914 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→22.33 Å / SU ML: 0.3475 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.9293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 6705 5.03 %RANDOM
Rwork0.1721 126696 --
obs0.1753 133401 96.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.36 Å2
Refinement stepCycle: LAST / Resolution: 2.65→22.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35216 0 80 109 35405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008936336
X-RAY DIFFRACTIONf_angle_d1.063249504
X-RAY DIFFRACTIONf_chiral_restr0.05615112
X-RAY DIFFRACTIONf_plane_restr0.00996544
X-RAY DIFFRACTIONf_dihedral_angle_d6.96254920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.680.3311450.22522830X-RAY DIFFRACTION64.42
2.68-2.720.3171670.22783240X-RAY DIFFRACTION73.84
2.72-2.750.30971810.23713385X-RAY DIFFRACTION77.76
2.75-2.780.3462120.23523766X-RAY DIFFRACTION86.31
2.78-2.820.31222290.2444115X-RAY DIFFRACTION93.84
2.82-2.860.3192300.24044234X-RAY DIFFRACTION97.11
2.86-2.90.35552100.23554324X-RAY DIFFRACTION98.18
2.9-2.940.31082310.22254262X-RAY DIFFRACTION98.86
2.94-2.990.27852170.21464444X-RAY DIFFRACTION99.36
2.99-3.040.29092110.21334383X-RAY DIFFRACTION99.7
3.04-3.090.29552260.21664361X-RAY DIFFRACTION99.91
3.09-3.150.27732260.21344392X-RAY DIFFRACTION99.96
3.15-3.210.29112230.19874385X-RAY DIFFRACTION99.93
3.21-3.270.26142390.19054388X-RAY DIFFRACTION99.94
3.27-3.340.24882490.18234345X-RAY DIFFRACTION99.89
3.34-3.420.25472340.17354405X-RAY DIFFRACTION99.94
3.42-3.510.2512240.16754362X-RAY DIFFRACTION99.96
3.51-3.60.21952530.15754358X-RAY DIFFRACTION99.87
3.6-3.710.21412110.16124430X-RAY DIFFRACTION99.98
3.71-3.820.22242150.15354410X-RAY DIFFRACTION99.94
3.82-3.960.21662480.14964382X-RAY DIFFRACTION99.85
3.96-4.120.20182390.14844349X-RAY DIFFRACTION99.83
4.12-4.30.19212440.13954358X-RAY DIFFRACTION99.76
4.3-4.530.19772220.13714418X-RAY DIFFRACTION99.76
4.53-4.810.1832580.14214354X-RAY DIFFRACTION99.74
4.81-5.180.18912020.1494438X-RAY DIFFRACTION99.89
5.18-5.690.2372310.16994384X-RAY DIFFRACTION99.94
5.69-6.50.21652280.16664410X-RAY DIFFRACTION99.78
6.5-8.120.21192640.17234399X-RAY DIFFRACTION99.74
8.12-22.330.19132360.15234385X-RAY DIFFRACTION98.17

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