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- PDB-6zj4: apo-Trehalose transferase (apo-TreT) from Thermoproteus uzoniensis -

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Basic information

Entry
Database: PDB / ID: 6zj4
Titleapo-Trehalose transferase (apo-TreT) from Thermoproteus uzoniensis
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: 2.1 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 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)45,6193
Polymers45,5031
Non-polymers1162
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SASDHG9
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-7 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.519, 68.776, 112.200
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 (archaea) / 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.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2019
RadiationMonochromator: Oxdouble crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→68.78 Å / Num. obs: 27351 / % possible obs: 96.8 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.053 / Rrim(I) all: 0.084 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.91-68.783.40.033890.9980.0240.03991.8
2.1-2.162.90.7321210.450.6480.9893.6

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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: 2x6q

2x6q


Resolution: 2.1→58.705 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.535 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.215 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.255 1336 4.89 %
Rwork0.208 25984 -
all0.197 --
obs-27320 95.88 %
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: 47.711 Å2
Baniso -1Baniso -2Baniso -3
1-1.979 Å20 Å2-0 Å2
2---1.053 Å20 Å2
3----0.926 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 6 107 3298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133300
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173154
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6454473
X-RAY DIFFRACTIONr_angle_other_deg1.2421.5797298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47121.033184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0261529
X-RAY DIFFRACTIONr_chiral_restr0.0670.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
X-RAY DIFFRACTIONr_nbd_refined0.1980.2638
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22908
X-RAY DIFFRACTIONr_nbtor_refined0.160.21596
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.29
X-RAY DIFFRACTIONr_nbd_other0.1650.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.24
X-RAY DIFFRACTIONr_mcbond_it3.5254.7941597
X-RAY DIFFRACTIONr_mcbond_other3.5184.791594
X-RAY DIFFRACTIONr_mcangle_it5.0987.181994
X-RAY DIFFRACTIONr_mcangle_other5.0977.1841995
X-RAY DIFFRACTIONr_scbond_it4.0875.3271703
X-RAY DIFFRACTIONr_scbond_other4.0475.3281702
X-RAY DIFFRACTIONr_scangle_it6.2547.7732475
X-RAY DIFFRACTIONr_scangle_other6.2217.7742474
X-RAY DIFFRACTIONr_lrange_it8.1455.8353640
X-RAY DIFFRACTIONr_lrange_other8.13255.7873628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.342890.3251820X-RAY DIFFRACTION91.7788
2.155-2.2140.344980.311841X-RAY DIFFRACTION95.9426
2.214-2.2780.2751120.2661810X-RAY DIFFRACTION98.1614
2.278-2.3480.306910.2471812X-RAY DIFFRACTION98.6522
2.348-2.4250.2831000.231709X-RAY DIFFRACTION98.5294
2.425-2.510.294800.2091672X-RAY DIFFRACTION98.0963
2.51-2.6040.256810.2081591X-RAY DIFFRACTION96.1472
2.604-2.7110.28980.2091555X-RAY DIFFRACTION98.7455
2.711-2.8310.276820.1991487X-RAY DIFFRACTION98.0013
2.831-2.9690.261700.2021439X-RAY DIFFRACTION97.1042
2.969-3.130.308690.2061365X-RAY DIFFRACTION96.8919
3.13-3.320.266540.2191265X-RAY DIFFRACTION95.2347
3.32-3.5490.29610.1931199X-RAY DIFFRACTION95.5994
3.549-3.8330.206600.1881100X-RAY DIFFRACTION93.9271
3.833-4.1980.207430.1611015X-RAY DIFFRACTION93.3804
4.198-4.6920.175440.14922X-RAY DIFFRACTION93.2432
4.692-5.4170.216380.152824X-RAY DIFFRACTION92.6882
5.417-6.630.259290.182692X-RAY DIFFRACTION91.4975
6.63-9.360.174230.164552X-RAY DIFFRACTION90.4088

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