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- PDB-6jbi: Structure of Tps1 apo structure -

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Basic information

Entry
Database: PDB / ID: 6jbi
TitleStructure of Tps1 apo structure
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 / ascospore formation / 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
Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, S. / Zhao, Y. / Yi, L. / 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 25, 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


Theoretical massNumber of molelcules
Total (without water)105,0252
Polymers105,0252
Non-polymers00
Water1629
1
A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase

A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)210,0514
Polymers210,0514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10080 Å2
ΔGint-35 kcal/mol
Surface area69940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.130, 121.480, 93.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 53.48 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→46.51 Å / Num. obs: 38668 / % possible obs: 97.7 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Net I/σ(I): 23.6
Reflection shellResolution: 2.5→2.5894 Å / Num. unique obs: 3843 / CC1/2: 0.859

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Processing

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

1uqt


Resolution: 2.5→29.716 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 1896 4.91 %
Rwork0.2264 --
obs0.2291 38642 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 0 9 7301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077482
X-RAY DIFFRACTIONf_angle_d1.1510162
X-RAY DIFFRACTIONf_dihedral_angle_d15.1494400
X-RAY DIFFRACTIONf_chiral_restr0.0661118
X-RAY DIFFRACTIONf_plane_restr0.0071304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56250.43561340.35672596X-RAY DIFFRACTION98
2.5625-2.63180.45441210.32622606X-RAY DIFFRACTION98
2.6318-2.70920.43251350.31512612X-RAY DIFFRACTION98
2.7092-2.79660.4161490.29312591X-RAY DIFFRACTION99
2.7966-2.89640.381320.29182453X-RAY DIFFRACTION92
2.8964-3.01230.38981480.28412581X-RAY DIFFRACTION98
3.0123-3.14920.32991360.26862613X-RAY DIFFRACTION99
3.1492-3.31510.36881350.25372664X-RAY DIFFRACTION99
3.3151-3.52250.29541360.23922635X-RAY DIFFRACTION99
3.5225-3.79390.27031340.22692662X-RAY DIFFRACTION99
3.7939-4.17480.25251300.20322605X-RAY DIFFRACTION97
4.1748-4.77680.22741150.18512627X-RAY DIFFRACTION96
4.7768-6.010.24441220.21652751X-RAY DIFFRACTION100
6.01-29.71790.23851690.19452750X-RAY DIFFRACTION97

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