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- PDB-6zn1: Trehalose transferase bound to alpha-D-glucopyranosyl-beta-galact... -

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Basic information

Entry
Database: PDB / ID: 6zn1
TitleTrehalose transferase bound to alpha-D-glucopyranosyl-beta-galactopyranose from Thermoproteus uzoniensis
ComponentsTrehalose phosphorylase/synthase
KeywordsTRANSFERASE / trehalose transferase / retaining glycosyltransferase / glycosidic bond formation
Function / homology
Function and homology information


glycosyltransferase activity / glucose metabolic process
Similarity search - Function
: / : / Trehalose synthase, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
beta-L-galactopyranose / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Trehalose phosphorylase/synthase
Similarity search - Component
Biological speciesThermoproteus uzoniensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 Catal / 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
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: 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

Downloads & links

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Assembly

Deposited unit
AAA: Trehalose phosphorylase/synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,41410
Polymers45,5031
Non-polymers9119
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, size-exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-2 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 68.771, 110.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules AAA

#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

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-GIV / beta-L-galactopyranose / beta-L-galactose / L-galactose / galactose


Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-galactopyranoseCOMMON NAMEGMML 1.0
b-L-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 150 molecules

#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: CNS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: Bis-Tris Propane, PEG 3350, potassium thiocyanide, 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 / Detector: PIXEL / Date: Sep 24, 2019
RadiationMonochromator: DCM Oxford-FMB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→60 Å / Num. obs: 47789 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 34.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.36
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 1.568 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4717 / CC1/2: 0.69 / % possible all: 99.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-Tret

Resolution: 1.75→58.509 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.204 / SU B: 3.086 / SU ML: 0.096 / Average fsc free: 0.889 / Average fsc work: 0.9015 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2345 2329 4.874 %
Rwork0.2021 45460 -
all0.204 --
obs-47789 99.985 %
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: 39.646 Å2
Baniso -1Baniso -2Baniso -3
1-1.109 Å20 Å2-0 Å2
2---1.346 Å20 Å2
3---0.238 Å2
Refinement stepCycle: LAST / Resolution: 1.75→58.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 56 143 3409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173237
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.654523
X-RAY DIFFRACTIONr_angle_other_deg1.2021.5847457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80621.326181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95315574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.471527
X-RAY DIFFRACTIONr_chiral_restr0.0570.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
X-RAY DIFFRACTIONr_nbd_refined0.2080.2624
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.22974
X-RAY DIFFRACTIONr_nbtor_refined0.160.21566
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2168
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.213
X-RAY DIFFRACTIONr_nbd_other0.30.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.210
X-RAY DIFFRACTIONr_mcbond_it2.394.0041605
X-RAY DIFFRACTIONr_mcbond_other2.3843.9981600
X-RAY DIFFRACTIONr_mcangle_it3.6285.9952000
X-RAY DIFFRACTIONr_mcangle_other3.6275.9972001
X-RAY DIFFRACTIONr_scbond_it2.6184.3561744
X-RAY DIFFRACTIONr_scbond_other2.6174.3561745
X-RAY DIFFRACTIONr_scangle_it4.0956.382522
X-RAY DIFFRACTIONr_scangle_other4.0946.3812523
X-RAY DIFFRACTIONr_lrange_it5.9946.1353624
X-RAY DIFFRACTIONr_lrange_other5.9946.143625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.3411990.3113292X-RAY DIFFRACTION100
1.795-1.8450.2951500.2923255X-RAY DIFFRACTION99.9706
1.845-1.8980.2881780.2653107X-RAY DIFFRACTION99.9696
1.898-1.9570.2731520.2463070X-RAY DIFFRACTION100
1.957-2.0210.2811480.2482960X-RAY DIFFRACTION100
2.021-2.0920.2881670.2342870X-RAY DIFFRACTION100
2.092-2.1710.2761370.2312767X-RAY DIFFRACTION100
2.171-2.2590.2481150.2152709X-RAY DIFFRACTION100
2.259-2.360.2171390.2062574X-RAY DIFFRACTION99.9632
2.36-2.4750.2381240.2122446X-RAY DIFFRACTION100
2.475-2.6080.3011190.2152335X-RAY DIFFRACTION100
2.608-2.7670.2281020.2122247X-RAY DIFFRACTION100
2.767-2.9570.2961100.2142086X-RAY DIFFRACTION100
2.957-3.1940.253870.2251984X-RAY DIFFRACTION99.9517
3.194-3.4990.2381000.2091790X-RAY DIFFRACTION100
3.499-3.9110.238780.1831655X-RAY DIFFRACTION100
3.911-4.5150.173630.1661481X-RAY DIFFRACTION100
4.515-5.5280.174600.1621274X-RAY DIFFRACTION100
5.528-7.8080.232680.183970X-RAY DIFFRACTION99.9038
7.808-580.167330.173588X-RAY DIFFRACTION99.679

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