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- PDB-8uag: Sucrose-phosphate synthase-like protein from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 8uag
TitleSucrose-phosphate synthase-like protein from Leishmania major
ComponentsSucrose-phosphate synthase-like protein
KeywordsSUGAR BINDING PROTEIN / Mannogen synthesis / sucrose-phosphate synthase / Leishmania major UDPG complex / LmjF.16.0950
Function / homologysucrose-phosphate synthase / sucrose-phosphate synthase activity / : / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Sucrose-phosphate synthase-like protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsGorman, M.A. / Parker, M.W. / McConville, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Sucrose-phosphate synthase-like protein from Leishmania major
Authors: Gorman, M.A. / Parker, M.W. / McConville, M.J. / Sernee, F. / Ralton, J.E. / Vinzenz, V. / Sani, M. / Soerianto, T.
History
DepositionSep 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sucrose-phosphate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3625
Polymers52,6471
Non-polymers7154
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.231, 59.689, 177.638
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Sucrose-phosphate synthase-like protein


Mass: 52646.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_16_0950 / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QES5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.28 % / Description: Thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22.5% v/v PEG Smear High, 10% v/v Ethylene Glycol, 0.1M MIB 4 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 23, 2023
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.29→44.41 Å / Num. obs: 19918 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 25.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.026 / Rrim(I) all: 0.085 / Χ2: 0.98 / Net I/σ(I): 19.6 / Num. measured all: 206017
Reflection shellResolution: 2.29→2.37 Å / % possible obs: 94.2 % / Redundancy: 10 % / Rmerge(I) obs: 0.244 / Num. measured all: 18314 / Num. unique obs: 1829 / CC1/2: 0.98 / Rpim(I) all: 0.079 / Rrim(I) all: 0.256 / Χ2: 0.92 / Net I/σ(I) obs: 8.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→44.41 Å / SU ML: 0.2525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 990 4.99 %
Rwork0.1562 18867 -
obs0.1601 19857 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.54 Å2
Refinement stepCycle: LAST / Resolution: 2.29→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 45 117 3816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01193822
X-RAY DIFFRACTIONf_angle_d1.1035185
X-RAY DIFFRACTIONf_chiral_restr0.0558552
X-RAY DIFFRACTIONf_plane_restr0.019670
X-RAY DIFFRACTIONf_dihedral_angle_d9.8179501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.410.30281340.18272540X-RAY DIFFRACTION96.22
2.41-2.570.25811400.17482682X-RAY DIFFRACTION99.96
2.57-2.760.26841380.1782649X-RAY DIFFRACTION100
2.76-3.040.31171340.18382695X-RAY DIFFRACTION100
3.04-3.480.2811550.17892684X-RAY DIFFRACTION99.96
3.48-4.390.20141430.13152732X-RAY DIFFRACTION99.9
4.39-44.410.17291460.13012885X-RAY DIFFRACTION99.64

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