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- PDB-6zj7: Trehalose transferase (TreT) from Thermoproteus uzoniensis soaked... -

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Basic information

Entry
Database: PDB / ID: 6zj7
TitleTrehalose transferase (TreT) from Thermoproteus uzoniensis soaked with Mg
ComponentsTrehalose phosphorylase/synthase
KeywordsTRANSFERASE / trehalose transferase / retaining glycosyltransferase / glycosidic bond formation
Function / homology: / : / Trehalose synthase, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / glucose metabolic process / THIOCYANATE ION / Trehalose phosphorylase/synthase
Function and homology information
Biological speciesThermoproteus uzoniensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBento, I. / Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.-H. / Hanefeld, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
European CommissionERA-IB-15-110 Germany
CitationJournal: Acs Catalysis / Year: 2020
Title: Anomeric Selectivity of Trehalose Transferase with Rare l-Sugars.
Authors: Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.L. / Bento, I. / Hanefeld, U.
History
DepositionJun 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Trehalose phosphorylase/synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1148
Polymers45,5031
Non-polymers6117
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-8 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.574, 69.277, 110.451
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Trehalose phosphorylase/synthase


Mass: 45503.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus uzoniensis (strain 768-20) (archaea)
Strain: 768-20 / Gene: TUZN_0976 / Production host: Escherichia coli (E. coli) / References: UniProt: F2L613
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2019
RadiationMonochromator: double-crystal monochromator FMB-OXFORD (Oxford, UK)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→110.45 Å / Num. obs: 25646 / % possible obs: 98.8 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Net I/σ(I): 17.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.024 / Num. unique obs: 2477 / CC1/2: 0.7 / Rpim(I) all: 0.013 / Rrim(I) all: 0.028

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-TreT

Resolution: 2.15→58.757 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.193 / SU B: 7.635 / SU ML: 0.188 / Average fsc free: 0.862 / Average fsc work: 0.8837 / Cross valid method: FREE R-VALUE / ESU R: 0.237 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2612 1311 5.112 %
Rwork0.1985 24335 -
all0.202 --
obs-25646 98.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.554 Å2
Baniso -1Baniso -2Baniso -3
1-3.601 Å20 Å2-0 Å2
2---2.509 Å20 Å2
3----1.092 Å2
Refinement stepCycle: LAST / Resolution: 2.15→58.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 37 88 3287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173142
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.6444431
X-RAY DIFFRACTIONr_angle_other_deg1.1511.5787269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39321.006179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68815572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2981528
X-RAY DIFFRACTIONr_chiral_restr0.0560.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined0.1950.2622
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.22965
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21505
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.25
X-RAY DIFFRACTIONr_nbd_other0.170.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.26
X-RAY DIFFRACTIONr_mcbond_it3.2685.3581578
X-RAY DIFFRACTIONr_mcbond_other3.2625.3571573
X-RAY DIFFRACTIONr_mcangle_it4.9278.0261965
X-RAY DIFFRACTIONr_mcangle_other4.9268.0271966
X-RAY DIFFRACTIONr_scbond_it3.545.841703
X-RAY DIFFRACTIONr_scbond_other3.5395.841704
X-RAY DIFFRACTIONr_scangle_it5.7678.562464
X-RAY DIFFRACTIONr_scangle_other5.7668.562465
X-RAY DIFFRACTIONr_lrange_it7.80861.343530
X-RAY DIFFRACTIONr_lrange_other7.81461.2783519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.348960.3021754X-RAY DIFFRACTION98.2475
2.206-2.2660.295970.2861685X-RAY DIFFRACTION98.0738
2.266-2.3320.295790.2651710X-RAY DIFFRACTION98.0274
2.332-2.4040.336790.2391633X-RAY DIFFRACTION98.2778
2.404-2.4830.315840.2421566X-RAY DIFFRACTION98.4487
2.483-2.570.323830.2221541X-RAY DIFFRACTION98.6035
2.57-2.6670.32720.2221474X-RAY DIFFRACTION98.6599
2.667-2.7750.256830.2031447X-RAY DIFFRACTION98.9651
2.775-2.8990.272680.191376X-RAY DIFFRACTION98.9041
2.899-3.040.254860.2031299X-RAY DIFFRACTION99.212
3.04-3.2040.3640.2191253X-RAY DIFFRACTION99.2464
3.204-3.3990.286710.2211198X-RAY DIFFRACTION99.2181
3.399-3.6330.273510.2021142X-RAY DIFFRACTION99.3339
3.633-3.9240.259640.1951045X-RAY DIFFRACTION99.3728
3.924-4.2980.235480.166986X-RAY DIFFRACTION99.3276
4.298-4.8040.217380.155905X-RAY DIFFRACTION99.2632
4.804-5.5450.181540.159784X-RAY DIFFRACTION98.9374
5.545-6.7870.311300.19683X-RAY DIFFRACTION99.4421
6.787-9.5810.207360.162536X-RAY DIFFRACTION99.6516

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