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- PDB-5huu: Structure of Candida albicans trehalose-6-phosphate synthase in c... -

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Basic information

Entry
Database: PDB / ID: 5huu
TitleStructure of Candida albicans trehalose-6-phosphate synthase in complex with UDP and glucose-6-phosphate
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
6-O-phosphono-alpha-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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: MBio / Year: 2017
Title: Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design.
Authors: Miao, Y. / Tenor, J.L. / Toffaletti, D.L. / Maskarinec, S.A. / Liu, J. / Lee, R.E. / Perfect, J.R. / 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 1.2Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 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)110,3716
Polymers109,0422
Non-polymers1,3294
Water1,00956
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)110,3716
Polymers109,0422
Non-polymers1,3294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_585-x,-y+3,z1
Buried area4510 Å2
ΔGint-27 kcal/mol
Surface area37200 Å2
2
A: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
B: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules

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)220,74212
Polymers218,0854
Non-polymers2,6578
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_585-x,-y+3,z1
Buried area13220 Å2
ΔGint-49 kcal/mol
Surface area70210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.682, 98.682, 188.885
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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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 (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: TPS1, CaO19.13961, CaO19.6640
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q92410, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 42031 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 51.88 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Χ2: 0.767 / Net I/av σ(I): 18.465 / Net I/σ(I): 8.7 / Num. measured all: 238628
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.37-2.414.60.63820140.8670.3260.7190.6197.3
2.41-2.455.40.621120.9190.2830.6640.567100
2.45-2.55.70.57420980.9230.2630.6330.568100
2.5-2.555.80.46721300.9380.2140.5140.596100
2.55-2.615.80.36920880.9610.1690.4070.584100
2.61-2.675.80.32721240.9650.1490.360.612100
2.67-2.745.80.27521090.9750.1260.3020.621100
2.74-2.815.80.23621000.9790.1080.260.616100
2.81-2.895.80.19120930.9840.0880.210.653100
2.89-2.995.80.15521070.9890.0710.170.671100
2.99-3.095.80.12921130.9920.060.1430.715100
3.09-3.225.80.11320980.9920.0520.1250.809100
3.22-3.365.80.09421060.9950.0440.1040.897100
3.36-3.545.80.08421180.9950.0380.0920.96599.9
3.54-3.765.80.06920900.9970.0320.0761.07299.9
3.76-4.055.70.0621110.9960.0280.0671.05699.6
4.05-4.465.70.05521160.9960.0250.060.94299.7
4.46-5.15.60.05120970.9980.0240.0561.01499.1
5.1-6.435.70.04621060.9980.0210.0510.81999.2
6.43-505.40.05821010.9960.0280.0640.91396.8

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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: 2.37→35.357 Å / FOM work R set: 0.7634 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1995 4.75 %
Rwork0.2003 39966 -
obs0.2025 41961 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.73 Å2 / Biso mean: 62.46 Å2 / Biso min: 32.16 Å2
Refinement stepCycle: final / Resolution: 2.37→35.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 0 126 56 7584
Biso mean--60.98 54.18 -
Num. residues----919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037665
X-RAY DIFFRACTIONf_angle_d0.67910397
X-RAY DIFFRACTIONf_chiral_restr0.0271150
X-RAY DIFFRACTIONf_plane_restr0.0031308
X-RAY DIFFRACTIONf_dihedral_angle_d13.0412809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.42930.33281340.26522778291298
2.4293-2.4950.31291420.259428502992100
2.495-2.56840.31221450.240128763021100
2.5684-2.65120.2941440.243128583002100
2.6512-2.7460.29411390.244928552994100
2.746-2.85590.32131440.248428613005100
2.8559-2.98580.3121440.242128713015100
2.9858-3.14310.2891400.240128733013100
3.1431-3.33990.26041450.228628342979100
3.3399-3.59750.29041460.220528623008100
3.5975-3.95910.19191420.183628893031100
3.9591-4.5310.2261430.16928643007100
4.531-5.70470.22011420.18112844298699
5.7047-35.36070.20971450.16952851299698

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