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- PDB-2wtx: Insight into the mechanism of enzymatic glycosyltransfer with ret... -

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Basic information

Entry
Database: PDB / ID: 2wtx
TitleInsight into the mechanism of enzymatic glycosyltransfer with retention through the synthesis and analysis of bisubstrate glycomimetics of trehalose-6-phosphate synthase
ComponentsALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
KeywordsTRANSFERASE / TREHALOSE SYNTHASE / GLYCOSYLTRANSFERASE / POTASSIUM / RETENTION / STRESS RESPONSE
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / response to osmotic stress / response to stress / DNA damage response
Similarity search - Function
Alpha,alpha-trehalose-phosphate synthase / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Chem-VDO / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsErrey, J.C. / Lee, S.S. / Gibson, R.P. / Martinez-Fleites, C. / Barry, C.S. / Jung, P.M.J. / OSullivan, A. / Davis, B.G. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Mechanistic Insight Into Enzymatic Glycosyl Transfer with Retention of Configuration Through Analysis of Glycomimetic Inhibitors.
Authors: Errey, J.C. / Lee, S.S. / Gibson, R.P. / Martinez Fleites, C. / Barry, C.S. / Jung, P.M.J. / O'Sullivan, A.C. / Davis, B.G. / Davies, G.J.
History
DepositionSep 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
B: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
C: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
D: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,29217
Polymers214,7044
Non-polymers3,58813
Water10,539585
1
B: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
C: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1158
Polymers107,3522
Non-polymers1,7636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-22.9 kcal/mol
Surface area35210 Å2
MethodPISA
2
A: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
D: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1779
Polymers107,3522
Non-polymers1,8257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-17.4 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.515, 120.287, 173.786
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
ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING] / TREHALOSE-6-PHOSPHATE SYNTHASE / UDP-GLUCOSE-GLUCOSEPHOSPHATE GLUCOSYLTRANSFERASE / OSMOREGULATORY ...TREHALOSE-6-PHOSPHATE SYNTHASE / UDP-GLUCOSE-GLUCOSEPHOSPHATE GLUCOSYLTRANSFERASE / OSMOREGULATORY TREHALOSE SYNTHESIS PROTEIN A


Mass: 53675.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P31677, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-VDO / [(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE


Mass: 415.330 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H26NO11P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.55 Å3/Da / Density % sol: 51 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. obs: 111567 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZ5

1gz5


Resolution: 2.2→98.91 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.365 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23473 5583 5 %RANDOM
Rwork0.19497 ---
obs0.19698 105869 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→98.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14489 0 228 585 15302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02215182
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.97320670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79951817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75823.911739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91152472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.86715105
X-RAY DIFFRACTIONr_chiral_restr0.1110.22264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111618
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6611.59067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.271214580
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86936115
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0834.56085
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 427 -
Rwork0.242 7591 -
obs--98.65 %

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