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

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Basic information

Entry
Database: PDB / ID: 9niq
TitleStructure of Candida albicans trehalose-6-phosphate synthase in complex with 4456
ComponentsAlpha,alpha-trehalose-phosphate synthase [UDP-forming]
KeywordsTRANSFERASE / inhibitor / complex / trehalose / fungal / thermotolerance
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: 3.35 Å
AuthorsWashington, 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)1P01AI104533 United States
CitationJournal: To Be Published
Title: Structure of Candida albicans trehalose-6-phosphate synthase in complex with 4456
Authors: Washington, E.J. / Brennan, R.G.
History
DepositionFeb 26, 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

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Assembly

Deposited unit
A: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8542
Polymers56,5541
Non-polymers2991
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.553, 117.553, 134.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 56554.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: TPS1, CAALFM_CR05720WA, CaO19.13961, CaO19.6640 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92410, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical ChemComp-A1BYI / N-[(4M)-4-(1-methyl-1H-pyrazol-4-yl)-1,3-thiazol-2-yl]-2-(pyridin-2-yl)acetamide


Mass: 299.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N5OS / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium sulfate, 0.1 M Tris-HCl pH 8.5 and 40% PEG400

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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: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 12398 Å / Relative weight: 1
ReflectionResolution: 3.35→58.78 Å / Num. obs: 75865 / % possible obs: 91.7 % / Redundancy: 9.9 % / CC1/2: 0.998 / Net I/σ(I): 14.87
Reflection shellResolution: 3.35→3.47 Å / Num. unique obs: 7778 / CC1/2: 0.932

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Processing

Software
NameVersionClassification
PHENIXv1.18.2-3874-000refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→58.78 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2893 716 9.37 %
Rwork0.2503 --
obs0.2541 7641 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→58.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 21 0 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023733
X-RAY DIFFRACTIONf_angle_d0.5345056
X-RAY DIFFRACTIONf_dihedral_angle_d4.596494
X-RAY DIFFRACTIONf_chiral_restr0.043553
X-RAY DIFFRACTIONf_plane_restr0.004645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.610.32971410.31191368X-RAY DIFFRACTION94
3.61-3.970.3341420.27191370X-RAY DIFFRACTION93
3.97-4.550.28961390.23451353X-RAY DIFFRACTION91
4.55-5.730.27771430.24461373X-RAY DIFFRACTION91
5.73-58.780.26271510.23181461X-RAY DIFFRACTION90

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