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

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Basic information

Entry
Database: PDB / ID: 8vrf
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: 1.74 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.
History
DepositionJan 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,93514
Polymers105,0372
Non-polymers1,89712
Water11,638646
1
B: Sucrose-phosphate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4417
Polymers52,5191
Non-polymers9236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Sucrose-phosphate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4937
Polymers52,5191
Non-polymers9756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.057, 92.709, 100.550
Angle α, β, γ (deg.)90.00, 120.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sucrose-phosphate synthase-like protein


Mass: 52518.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_16_0950 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QES5, sucrose-phosphate synthase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.52 Å3/Da / Density % sol: 51.25 % / Description: Thick rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 26% PEG 3350, 200 mM Magnesium Chloride, 1mM UDPG, Protein crystal seeds

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953733 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953733 Å / Relative weight: 1
ReflectionResolution: 1.74→48.05 Å / Num. obs: 104260 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 13.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4988 / CC1/2: 0.705 / Rpim(I) all: 0.379 / Rrim(I) all: 0.722 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→48.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.666 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21102 5262 5 %RANDOM
Rwork0.17904 ---
obs0.1807 98986 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.921 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0.14 Å2
2--1.44 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.74→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7268 0 117 646 8031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127678
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167059
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.82510423
X-RAY DIFFRACTIONr_angle_other_deg0.5911.7616328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.938537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83101265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021785
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1732.3773700
X-RAY DIFFRACTIONr_mcbond_other2.1652.3773700
X-RAY DIFFRACTIONr_mcangle_it2.9584.2634639
X-RAY DIFFRACTIONr_mcangle_other2.9594.2644640
X-RAY DIFFRACTIONr_scbond_it3.0712.6783978
X-RAY DIFFRACTIONr_scbond_other3.072.6783979
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6984.7665785
X-RAY DIFFRACTIONr_long_range_B_refined5.73424.068712
X-RAY DIFFRACTIONr_long_range_B_other5.73324.068713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 382 -
Rwork0.259 7145 -
obs--97.03 %

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