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- PDB-6jbw: Structure of Tps1/UDP complex -

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Basic information

Entry
Database: PDB / ID: 6jbw
TitleStructure of Tps1/UDP complex
ComponentsTrehalose-6-phosphate synthase
KeywordsTRANSFERASE / Trehalose-6-phosphate synthase
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / 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
URIDINE-5'-DIPHOSPHATE / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesPyricularia oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWang, S. / Zhao, Y. / Wang, D. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Ministry of Science and Technology (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 1.1Nov 22, 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

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Assembly

Deposited unit
A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8344
Polymers105,0252
Non-polymers8082
Water90150
1
A: Trehalose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9172
Polymers52,5131
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-7 kcal/mol
Surface area19780 Å2
MethodPISA
2
B: Trehalose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9172
Polymers52,5131
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-7 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.751, 99.295, 121.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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


Mass: 52512.719 Da / Num. of mol.: 2
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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
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: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.65→45.97 Å / Num. obs: 33303 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.023 / Net I/σ(I): 36.55
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 3263 / CC1/2: 0.959

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UQU

1uqu


Resolution: 2.65→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.258 1535 4.6 %
Rwork0.21 --
obs0.212 33280 99.7 %
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 50 50 7392
LS refinement shellResolution: 2.65→2.745 Å
RfactorNum. reflection% reflection
Rfree0.554 --
Rwork0.506 3261 -
obs--100 %

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