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- PDB-5huv: Structure of Candida albicans trehalose-6-phosphate synthase E341... -

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Basic information

Entry
Database: PDB / ID: 5huv
TitleStructure of Candida albicans trehalose-6-phosphate synthase E341R/E346R in complex with UDP-glucose
ComponentsAlpha,alpha-trehalose-phosphate synthase [UDP-forming]
KeywordsTRANSFERASE / trehalose-6-phosphate synthase
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) / filamentous growth of a population of unicellular organisms in response to biotic stimulus / cellular response to desiccation / trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / trehalose metabolism in response to stress / filamentous growth / cellular response to heat
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-GLUCOSE / Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsMiao, Y. / Brennan, R.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1P01AI104533-01A1 United States
CitationJournal: To Be Published
Title: Structure of Candida albicans trehalose-6-phosphate synthase E341R/E346R in complex with UDP-glucose
Authors: Miao, Y. / Brennan, R.G.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)110,2874
Polymers109,1552
Non-polymers1,1332
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-15 kcal/mol
Surface area37480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.638, 98.638, 186.592
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-888-

HOH

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Components

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


Mass: 54577.336 Da / Num. of mol.: 2 / Mutation: E341R/E346R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M lithium sulfate, 0.1 M Tris, 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.27
ReflectionResolution: 2→50 Å / Num. obs: 69000 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Rrim(I) all: 0.098 / Χ2: 1.629 / Net I/av σ(I): 31.5 / Net I/σ(I): 10.3 / Num. measured all: 514978
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.037.50.44334440.9030.1730.4760.818100
2.03-2.077.50.38434360.9320.150.4130.888100
2.07-2.117.50.33934360.9390.1320.3640.913100
2.11-2.157.50.29434680.950.1150.3160.989100
2.15-2.27.50.26134160.9610.1020.281.011100
2.2-2.257.50.23634340.9680.0920.2531.094100
2.25-2.317.50.21334460.9820.0830.2291.087100
2.31-2.377.50.18734430.9770.0730.2011.176100
2.37-2.447.50.16434440.9820.0640.1761.199100
2.44-2.527.50.14934590.9860.0580.161.232100
2.52-2.617.60.12934350.9880.050.1381.328100
2.61-2.717.60.11234600.9910.0440.1211.366100
2.71-2.847.60.10534320.9920.0410.1121.47100
2.84-2.997.50.09134630.9960.0350.0981.754100
2.99-3.177.50.08634440.9940.0340.0932.283100
3.17-3.427.30.0834510.9940.0320.0863.032100
3.42-3.767.10.07234500.9950.0290.0783.467100
3.76-4.317.20.06334600.9960.0250.0673.39799.9
4.31-5.437.30.04934660.9980.020.0532.418100
5.43-507.60.04335130.9980.0170.0461.917100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Candida albicans Tps1

Resolution: 2.002→49.319 Å / FOM work R set: 0.8481 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1705 2017 2.93 %
Rwork0.1447 66831 -
obs0.1465 68938 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.09 Å2 / Biso mean: 26.92 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 2.002→49.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7513 0 116 735 8364
Biso mean--25.52 36.53 -
Num. residues----933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077770
X-RAY DIFFRACTIONf_angle_d1.10710534
X-RAY DIFFRACTIONf_chiral_restr0.0451166
X-RAY DIFFRACTIONf_plane_restr0.0051326
X-RAY DIFFRACTIONf_dihedral_angle_d12.1462860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 97 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0029-2.05290.22181460.1847914937
2.0529-2.10840.21430.173947884931
2.1084-2.17040.19511420.168547164858
2.1704-2.24050.19661440.163247884932
2.2405-2.32050.20391390.159647534892
2.3205-2.41330.17371470.158947554902
2.4133-2.52310.19321470.160647654912
2.5231-2.6560.16861450.150847574902
2.656-2.82220.20241370.159547854922
2.8222-3.03980.1991390.152447684907
3.0398-3.34520.17341470.145347734920
3.3452-3.8280.16821480.128747884936
3.828-4.8180.14171450.11547714916
4.818-26.30790.13931480.139148334981

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