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- PDB-9nkb: Structure of Candida albicans trehalose-6-phosphate synthase in c... -

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Basic information

Entry
Database: PDB / ID: 9nkb
TitleStructure of Candida albicans trehalose-6-phosphate synthase in complex with SJ6675
ComponentsAlpha,alpha-trehalose-phosphate synthase [UDP-forming]
KeywordsTRANSFERASE / inhibitor / complex / fungal pathogen / thermotolerance / stress
Function / homology
Function and homology information


filamentous growth of a population of unicellular organisms in response to heat / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / cellular response to desiccation / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / filamentous growth of a population of unicellular organisms in response to biotic stimulus / trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / filamentous growth / cellular response to stress / cellular response to heat
Similarity search - Function
Alpha,alpha-trehalose-phosphate synthase / Glycosyl transferase, family 20 / Glycosyltransferase family 20
Similarity search - Domain/homology
: / Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSchaefer, M. / Washington, E.J. / Brennan, R.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Inhibitors of trehalose-6-phosphate synthase activity in fungal pathogens compromise thermal tolerance pathways
Authors: Washington, E.J. / Brennan, R.G.
History
DepositionFeb 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3754
Polymers109,0422
Non-polymers3322
Water00
1
A: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules

B: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3754
Polymers109,0422
Non-polymers3322
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_654x-y+1,x,z-1/61
Buried area2460 Å2
ΔGint-8 kcal/mol
Surface area37110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.051, 115.051, 266.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Alpha,alpha-trehalose-phosphate synthase [UDP-forming] / Trehalose-6-phosphate synthase / UDP-glucose-glucosephosphate glucosyltransferase


Mass: 54521.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: TPS1, CaO19.13961, CaO19.6640 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92410, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical ChemComp-A1BYV / (4P)-4-(furan-3-yl)-1,3-thiazol-2-amine


Mass: 166.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2OS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) PEG 400, 0.2M MgSO4, 2% (v/v) glycerol, 0.1M Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 12398 eV
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 12398 Å / Relative weight: 1
ReflectionResolution: 3.5→47.05 Å / Num. obs: 13858 / % possible obs: 99.52 % / Redundancy: 11.4 % / CC1/2: 1 / Net I/σ(I): 21.77
Reflection shellResolution: 3.5→3.626 Å / Num. unique obs: 1326 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874:000)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→47.05 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 1367 9.9 %
Rwork0.2407 --
obs0.2441 13813 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7474 0 22 0 7496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047678
X-RAY DIFFRACTIONf_angle_d0.6810398
X-RAY DIFFRACTIONf_dihedral_angle_d9.4471010
X-RAY DIFFRACTIONf_chiral_restr0.0461140
X-RAY DIFFRACTIONf_plane_restr0.0051326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.630.371330.32011191X-RAY DIFFRACTION99
3.63-3.770.36311110.31861228X-RAY DIFFRACTION100
3.77-3.940.31711170.30941226X-RAY DIFFRACTION100
3.94-4.150.31131260.25361240X-RAY DIFFRACTION100
4.15-4.410.27331440.24311217X-RAY DIFFRACTION100
4.41-4.750.29171650.24551206X-RAY DIFFRACTION100
4.75-5.230.26971440.2281232X-RAY DIFFRACTION100
5.23-5.980.29891400.24761252X-RAY DIFFRACTION100
5.98-7.530.26251480.23451273X-RAY DIFFRACTION100
7.54-47.050.19471390.17711381X-RAY DIFFRACTION98

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