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- PDB-1uqu: Trehalose-6-phosphate from E. coli bound with UDP-glucose. -

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Basic information

Entry
Database: PDB / ID: 1uqu
TitleTrehalose-6-phosphate from E. coli bound with UDP-glucose.
ComponentsALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
KeywordsSYNTHASE / GLYCOSYLTRANSFERASE / TRANSFERASE
Function / homology
Function and homology information


trehalose metabolism in response to cold stress / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / response to stress / response to osmotic 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-GLUCOSE / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGibson, R.P. / Tarling, C.A. / Roberts, S. / Withers, S.G. / Davies, G.J.
Citation
Journal: J. Biol. Chem. / Year: 2004
Title: The donor subsite of trehalose-6-phosphate synthase: binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 A resolution.
Authors: Gibson, R.P. / Tarling, C.A. / Roberts, S. / Withers, S.G. / Davies, G.J.
#1: Journal: Chem.Biol. / Year: 2002
Title: Insights Into Trehalose Synthesis Provided by the Structure of the Retaining Glycosyltransferase Otsa
Authors: Gibson, R.P. / Turkenburg, J.P. / Charnock, S.J. / Lloyd, R. / Davies, G.J.
History
DepositionOct 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 2, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Mar 4, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: database_PDB_caveat / diffrn_source ...database_PDB_caveat / diffrn_source / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type / _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
B: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0613
Polymers109,4942
Non-polymers5661
Water1,71195
1
A: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
B: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
hetero molecules

A: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
B: ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,1216
Polymers218,9884
Non-polymers1,1332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9920 Å2
ΔGint-44 kcal/mol
Surface area67660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.905, 102.310, 118.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.87957, -0.47576, -0.00329), (-0.47497, -0.87846, 0.05202), (-0.02764, -0.0442, -0.99864)
Vector: 6.11164, 19.15926, 58.43347)

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Components

#1: Protein ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE / TREHALOSE-6-PHOSPHATE SYNTHASE / UDP-GLUCOSE-GLUCOSEPHOSPHATE GLUCOSYLTRANSFERASE


Mass: 54747.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: C-TERMINAL 6XHIS-TAG / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P31677, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMODIFIED C-TERMINAL FOR OVER-EXPRESSION.

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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: 2.4 Å3/Da / Density % sol: 49.3 %
Crystal growpH: 8
Details: 30% PEG 4000, 200MM AMMONIUM ACETATE, 100MM TRISHCL PH 8
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.
2200 mM1dropNaCl
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 69411 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.79 / % possible all: 68
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 68 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.79

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZ5

1gz5


Resolution: 2→19.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.669 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3507 5.1 %RANDOM
Rwork0.232 ---
obs0.234 65900 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7229 0 36 95 7360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.491.95710106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025709
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.23399
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5761.54483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04627204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84132949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7874.52902
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 201
Rwork0.299 3359
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.49

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