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- PDB-5hus: Structure of Candida albicans trehalose synthase regulatory prote... -

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Basic information

Entry
Database: PDB / ID: 5hus
TitleStructure of Candida albicans trehalose synthase regulatory protein C-terminal domain
Componentstrehalose synthase regulatory protein
KeywordsTRANSFERASE / trehalose synthase regulatory protein
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose metabolism in response to stress / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process
Similarity search - Function
Trehalose-phosphatase / Trehalose-phosphatase / Glycosyl transferase, family 20 / Glycosyltransferase family 20
Similarity search - Domain/homology
Trehalose 6-phosphate synthase/phosphatase complex subunit / :
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.751 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 synthase regulatory protein C-terminal domain
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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: trehalose synthase regulatory protein


Theoretical massNumber of molelcules
Total (without water)33,9061
Polymers33,9061
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.940, 106.940, 41.886
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein trehalose synthase regulatory protein


Mass: 33906.301 Da / Num. of mol.: 1
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: TPS3, CaO19.12808, CaO19.5348 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5A5Q1, UniProt: A0A1D8PIS4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate, 20% PEG 4000, 10% 2-propanol

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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: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 27807 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.036 / Rrim(I) all: 0.081 / Χ2: 1.219 / Net I/av σ(I): 33.333 / Net I/σ(I): 8.7 / Num. measured all: 149128
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.783.60.3613570.8910.2120.420.43100
1.78-1.814.80.34714150.9380.1770.3910.446100
1.81-1.855.20.3413670.9490.1650.3780.466100
1.85-1.895.30.29213800.9610.140.3250.488100
1.89-1.935.40.23413550.9780.1110.260.516100
1.93-1.975.50.20913960.9810.0990.2320.607100
1.97-2.025.50.16413900.980.0770.1810.643100
2.02-2.075.50.14213580.9880.0670.1570.758100
2.07-2.145.50.12314040.9890.0580.1360.819100
2.14-2.25.60.11513970.9910.0540.1270.911100
2.2-2.285.50.10213740.9920.0480.1130.995100
2.28-2.385.60.09913870.9910.0470.1091.131100
2.38-2.485.60.0913890.9930.0430.11.204100
2.48-2.615.60.08414000.9910.040.0931.314100
2.61-2.785.60.07413760.9940.0360.0831.32899.9
2.78-2.995.60.07213990.9920.0340.081.59299.9
2.99-3.295.50.07214000.9930.0350.0812.12899.9
3.29-3.775.50.06614060.9940.0320.0742.67299.7
3.77-4.755.40.05814060.9950.0290.0652.65899.3
4.75-505.20.05914510.9950.0290.0662.72898.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.751→32.973 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.2168 2000 7.2 %
Rwork0.1857 --
obs0.188 27779 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.95 Å2 / Biso mean: 33.22 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 1.751→32.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 0 228 2528
Biso mean---39.6 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042336
X-RAY DIFFRACTIONf_angle_d0.7943164
X-RAY DIFFRACTIONf_chiral_restr0.032374
X-RAY DIFFRACTIONf_plane_restr0.003404
X-RAY DIFFRACTIONf_dihedral_angle_d13.798860
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 (%)
1.7508-1.79460.23931380.215918391977100
1.7946-1.84310.23921430.215618151958100
1.8431-1.89730.30181410.219618271968100
1.8973-1.95850.25261370.205718201957100
1.9585-2.02850.26131460.198718401986100
2.0285-2.10970.23821430.190318341977100
2.1097-2.20570.24221440.188718431987100
2.2057-2.3220.22321420.184518341976100
2.322-2.46740.21991470.191118271974100
2.4674-2.65790.23151440.198118451989100
2.6579-2.92520.28511390.198818391978100
2.9252-3.34810.18561450.193118531998100
3.3481-4.21690.18171450.168718742019100
4.2169-32.97930.19731460.17111889203599

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