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- PDB-6jbr: Tps1/UDP/T6P complex -

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Basic information

Entry
Database: PDB / ID: 6jbr
TitleTps1/UDP/T6P complex
ComponentsTrehalose-6-phosphate synthase
KeywordsTRANSFERASE / Trehalose-6-phosphate synthase
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / ascospore formation / trehalose biosynthetic process / trehalose metabolism in response to stress / cellular response to heat / nucleotide binding / cytosol
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
trehalose-6-phosphate / URIDINE-5'-DIPHOSPHATE / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesPyricularia oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsWang, S. / Zhao, Y. / Wang, D. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFD0300700 China
CitationJournal: Biochem.J. / Year: 2019
Title: Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1.
Authors: Wang, S. / Zhao, Y. / Yi, L. / Shen, M. / Wang, C. / Zhang, X. / Yang, J. / Peng, Y.L. / Wang, D. / Liu, J.
History
DepositionJan 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase
D: Trehalose-6-phosphate synthase
F: Trehalose-6-phosphate synthase
H: Trehalose-6-phosphate synthase
K: Trehalose-6-phosphate synthase
M: Trehalose-6-phosphate synthase
O: Trehalose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)426,71324
Polymers420,1028
Non-polymers6,61216
Water34,5891920
1
A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase
D: Trehalose-6-phosphate synthase
O: Trehalose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,35712
Polymers210,0514
Non-polymers3,3068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-21 kcal/mol
Surface area65900 Å2
MethodPISA
2
H: Trehalose-6-phosphate synthase
K: Trehalose-6-phosphate synthase
hetero molecules

F: Trehalose-6-phosphate synthase
hetero molecules

M: Trehalose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,35712
Polymers210,0514
Non-polymers3,3068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area12250 Å2
ΔGint-18 kcal/mol
Surface area65770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.279, 172.493, 141.703
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Trehalose-6-phosphate synthase / UDP-glucose-glucosephosphate glucosyltransferase


Mass: 52512.719 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae 70-15 (fungus) / Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_03860 / Production host: Escherichia coli (E. coli)
References: UniProt: G4NHF4, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Polysaccharide
6-O-phosphono-alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose-6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1a_1-5_6*OPO/3O/3=O]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1920 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, 20% PEG 3350 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 305744 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Net I/σ(I): 32.26
Reflection shellResolution: 2.03→2.1 Å / Rmerge(I) obs: 0.451 / Num. unique obs: 30304 / CC1/2: 0.892 / Rpim(I) all: 0.195

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UQT

1uqt


Resolution: 2.03→29.798 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.234 14918 4.88 %
Rwork0.211 --
obs0.212 305727 99.64 %
Refinement stepCycle: LAST / Resolution: 2.03→29.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29680 0 416 1920 32016
LS refinement shellResolution: 2.03→2.05 Å
RfactorNum. reflection% reflection
Rfree0.278 439 -
Rwork0.248 9395 -
obs--97 %

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