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- PDB-8z2r: Crystal structure of trehalose synthase mutant N253T from Deinoco... -

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Basic information

Entry
Database: PDB / ID: 8z2r
TitleCrystal structure of trehalose synthase mutant N253T 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: 2.53 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)521,29132
Polymers519,7998
Non-polymers1,49224
Water8,359464
1
A: maltose alpha-D-glucosyltransferase
C: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3238
Polymers129,9502
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-10 kcal/mol
Surface area37160 Å2
MethodPISA
2
B: maltose alpha-D-glucosyltransferase
F: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3238
Polymers129,9502
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-45 kcal/mol
Surface area36920 Å2
MethodPISA
3
D: maltose alpha-D-glucosyltransferase
G: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3238
Polymers129,9502
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-21 kcal/mol
Surface area37350 Å2
MethodPISA
4
E: maltose alpha-D-glucosyltransferase
H: maltose alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3238
Polymers129,9502
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-33 kcal/mol
Surface area37310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.599, 195.382, 131.317
Angle α, β, γ (deg.)90.000, 92.820, 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: 64974.844 Da / Num. of mol.: 8 / Mutation: N253T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (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.: 464 / 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: 2.53→30 Å / Num. obs: 146481 / % possible obs: 99.8 % / Redundancy: 2.2 % / Biso Wilson estimate: 37.45 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 5.2
Reflection shellResolution: 2.53→2.59 Å / Rmerge(I) obs: 0.22 / Num. unique obs: 146481

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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: 2.53→27.79 Å / SU ML: 0.454 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.2758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.29 7454 5.09 %
Rwork0.2169 139027 -
obs0.2207 146481 91.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.22 Å2
Refinement stepCycle: LAST / Resolution: 2.53→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35224 0 80 464 35768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009336344
X-RAY DIFFRACTIONf_angle_d1.10549520
X-RAY DIFFRACTIONf_chiral_restr0.05625120
X-RAY DIFFRACTIONf_plane_restr0.01026544
X-RAY DIFFRACTIONf_dihedral_angle_d7.09034920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.560.38041430.27612376X-RAY DIFFRACTION47.13
2.56-2.590.33331980.27513211X-RAY DIFFRACTION64.07
2.59-2.620.38891850.26693423X-RAY DIFFRACTION68.11
2.62-2.650.36122040.27233616X-RAY DIFFRACTION70.9
2.65-2.690.34031820.27773855X-RAY DIFFRACTION76.39
2.69-2.720.37042170.29594012X-RAY DIFFRACTION79.3
2.72-2.760.38842110.29164200X-RAY DIFFRACTION83.12
2.76-2.80.3782620.29514444X-RAY DIFFRACTION87.88
2.8-2.850.38052490.30124724X-RAY DIFFRACTION93.39
2.85-2.890.37552780.29714933X-RAY DIFFRACTION97.46
2.89-2.940.42282710.28244954X-RAY DIFFRACTION98.64
2.94-30.34442610.27365033X-RAY DIFFRACTION98.93
3-3.050.37092590.26645043X-RAY DIFFRACTION98.95
3.05-3.120.36882520.27265005X-RAY DIFFRACTION99.06
3.12-3.180.32652390.26485104X-RAY DIFFRACTION99.18
3.18-3.260.33472540.24524973X-RAY DIFFRACTION99.17
3.26-3.340.36592580.25185026X-RAY DIFFRACTION99.12
3.34-3.430.32972970.24595007X-RAY DIFFRACTION99.05
3.43-3.530.33312630.23045028X-RAY DIFFRACTION98.93
3.53-3.640.2962750.21095015X-RAY DIFFRACTION98.95
3.64-3.770.28172670.20085019X-RAY DIFFRACTION99.14
3.77-3.920.25652550.19535024X-RAY DIFFRACTION98.86
3.92-4.10.23862630.18625048X-RAY DIFFRACTION99.12
4.1-4.320.25282860.17844986X-RAY DIFFRACTION98.82
4.32-4.590.2383070.17234993X-RAY DIFFRACTION98.6
4.59-4.940.22052560.17075004X-RAY DIFFRACTION98.32
4.94-5.430.27772670.18265012X-RAY DIFFRACTION98.53
5.43-6.210.26262280.18255046X-RAY DIFFRACTION98.25
6.21-7.80.22782690.17355022X-RAY DIFFRACTION98.05
7.8-27.790.19692980.16374891X-RAY DIFFRACTION95.39

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