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- PDB-8z2t: Crystal structure of trehalose synthase from Deinococcus radiodur... -

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Basic information

Entry
Database: PDB / ID: 8z2t
TitleCrystal structure of trehalose synthase from Deinococcus radiodurans complexed with validoxylamine A (VAA)
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
Chem-VDM / maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,55016
Polymers259,9514
Non-polymers1,59912
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-24 kcal/mol
Surface area36870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.276, 153.247, 154.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 64987.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (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.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-VDM / (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL / VALIDOXYLAMINE


Mass: 335.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H25NO8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Imidazole (pH6.5) and 1.0M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / 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: 2.83→30 Å / Num. obs: 76836 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 52.04 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.5
Reflection shellResolution: 2.83→2.93 Å / Rmerge(I) obs: 0.178 / Num. unique obs: 76836

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→29.99 Å / SU ML: 0.3821 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.33
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 3661 4.86 %
Rwork0.1777 71728 -
obs0.1802 75389 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.4 Å2
Refinement stepCycle: LAST / Resolution: 2.83→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17616 0 100 101 17817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008518244
X-RAY DIFFRACTIONf_angle_d1.028524868
X-RAY DIFFRACTIONf_chiral_restr0.05362592
X-RAY DIFFRACTIONf_plane_restr0.00923276
X-RAY DIFFRACTIONf_dihedral_angle_d16.88096792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.870.359930.3131826X-RAY DIFFRACTION65.83
2.87-2.910.36251160.27822472X-RAY DIFFRACTION88.45
2.91-2.950.33421250.25112720X-RAY DIFFRACTION96.18
2.95-2.990.2711380.2452725X-RAY DIFFRACTION98.42
2.99-3.040.33821400.24682755X-RAY DIFFRACTION98.84
3.04-3.090.27951540.23782772X-RAY DIFFRACTION99.29
3.09-3.140.31611380.22552788X-RAY DIFFRACTION99.52
3.14-3.20.28931450.21112785X-RAY DIFFRACTION99.8
3.2-3.260.27851230.21752802X-RAY DIFFRACTION99.73
3.26-3.330.26221420.22252786X-RAY DIFFRACTION99.66
3.33-3.40.28451270.2272816X-RAY DIFFRACTION99.8
3.4-3.480.29271360.21022803X-RAY DIFFRACTION99.8
3.48-3.560.25531430.20262805X-RAY DIFFRACTION99.76
3.56-3.660.28061510.19222791X-RAY DIFFRACTION99.66
3.66-3.770.23761480.18162798X-RAY DIFFRACTION99.73
3.77-3.890.23671360.17332823X-RAY DIFFRACTION99.83
3.89-4.030.20891500.15912806X-RAY DIFFRACTION99.83
4.03-4.190.19861260.15712826X-RAY DIFFRACTION99.7
4.19-4.380.1721590.14542795X-RAY DIFFRACTION99.8
4.38-4.610.18491330.13562825X-RAY DIFFRACTION99.9
4.61-4.90.18461560.14272841X-RAY DIFFRACTION99.77
4.9-5.270.20771460.14132838X-RAY DIFFRACTION99.67
5.27-5.80.21411680.15422806X-RAY DIFFRACTION99.73
5.8-6.630.19161310.15252892X-RAY DIFFRACTION99.31
6.63-8.320.21351770.16242848X-RAY DIFFRACTION99.47
8.33-29.990.16851600.14482984X-RAY DIFFRACTION98.62

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