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- PDB-5gtw: The N253R mutant structures of trehalose synthase from Deinococcu... -

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Basic information

Entry
Database: PDB / ID: 5gtw
TitleThe N253R mutant structures of trehalose synthase from Deinococcus radiodurans display two different active-site conformations
ComponentsTrehalose synthase
KeywordsISOMERASE / Trehalose synthase / Glycoside hydrolase family 13
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 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsChow, S.Y. / Wei, Y.J. / Liaw, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyMOST 103-2311-B-010-005 Taiwan
CitationJournal: To Be Published
Title: The N253R mutant structures of trehalose synthase from Deinococcus radiodurans display two different active-site conformations
Authors: Chow, S.Y. / Wei, Y.J. / Liaw, S.H.
History
DepositionAug 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trehalose synthase
B: Trehalose synthase
C: Trehalose synthase
D: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,74815
Polymers260,1244
Non-polymers62411
Water2,792155
1
A: Trehalose synthase
D: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3137
Polymers130,0622
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area38970 Å2
MethodPISA
2
B: Trehalose synthase
C: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4358
Polymers130,0622
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-20 kcal/mol
Surface area37730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.383, 134.058, 197.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Trehalose synthase


Mass: 65030.938 Da / Num. of mol.: 4 / Mutation: R97W,N253R,T313I,I380V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% PEG 4000, 0.2M sodium acetate trihydrate, 0.3 M Tris-HCl (pH 7.0)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→20 Å / Num. obs: 54418 / % possible obs: 96.2 % / Redundancy: 3.6 % / Net I/σ(I): 11.8
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tvu

4tvu


Resolution: 2.93→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.879 / SU B: 22.359 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26676 2696 5 %RANDOM
Rwork0.18169 ---
obs0.18592 51664 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.392 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å20 Å20 Å2
2--0.32 Å20 Å2
3----4.85 Å2
Refinement stepCycle: 1 / Resolution: 2.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17628 0 32 155 17815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918181
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216582
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.95524767
X-RAY DIFFRACTIONr_angle_other_deg0.85338090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98552188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37823.205936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.999152768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.45415156
X-RAY DIFFRACTIONr_chiral_restr0.0810.22559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5595.328767
X-RAY DIFFRACTIONr_mcbond_other3.5535.3198766
X-RAY DIFFRACTIONr_mcangle_it5.6117.97210948
X-RAY DIFFRACTIONr_mcangle_other5.6117.97210949
X-RAY DIFFRACTIONr_scbond_it3.6195.6289414
X-RAY DIFFRACTIONr_scbond_other3.6195.6289414
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7828.32913820
X-RAY DIFFRACTIONr_long_range_B_refined8.51643.01121049
X-RAY DIFFRACTIONr_long_range_B_other8.51443.01321040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.925→2.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 167 -
Rwork0.305 3335 -
obs--85.44 %

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