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- PDB-9dcm: Sucrose-phosphate synthase from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 9dcm
TitleSucrose-phosphate synthase from Leishmania major
ComponentsSucrose-phosphate synthase-like protein
KeywordsSUGAR BINDING PROTEIN / Glycosyltransferase / mannogen synthesis / Leishmania / sucrose-phosphate synthase
Function / homologysucrose-phosphate synthase / sucrose-phosphate synthase activity / : / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / URIDINE-5'-DIPHOSPHATE / Sucrose-phosphate synthase-like protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsGorman, M.A. / Parker, M.W. / McConville, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Sucrose-phosphate synthase from Leishmania major
Authors: Gorman, M.A. / Parker, M.W. / McConville, M.J.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,5216
Polymers104,6332
Non-polymers8884
Water00
1
B: Sucrose-phosphate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7613
Polymers52,3161
Non-polymers4442
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Sucrose-phosphate synthase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7613
Polymers52,3161
Non-polymers4442
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)216.895, 216.895, 216.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Sucrose-phosphate synthase-like protein


Mass: 52316.434 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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
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: 4.08 Å3/Da / Density % sol: 69.89 % / Description: Cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18 -22% PEG3350, 100 mM Bis-Tris pH 5.5 and 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953729 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953729 Å / Relative weight: 1
ReflectionResolution: 3.11→49.76 Å / Num. obs: 59252 / % possible obs: 99.8 % / Redundancy: 78 % / Biso Wilson estimate: 39.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.346 / Rpim(I) all: 0.039 / Net I/σ(I): 21.7
Reflection shellResolution: 3.11→3.27 Å / Redundancy: 72.6 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4515 / CC1/2: 0.917 / Rpim(I) all: 0.186 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5109: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→49.76 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 3101 5.23 %
Rwork0.1762 --
obs0.179 59252 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7321 0 52 0 7373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d17.0332756
X-RAY DIFFRACTIONf_chiral_restr0.0611088
X-RAY DIFFRACTIONf_plane_restr0.0131329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.150.37081310.2862402X-RAY DIFFRACTION95
3.16-3.210.35921250.26042595X-RAY DIFFRACTION100
3.21-3.260.3071710.24592520X-RAY DIFFRACTION100
3.26-3.320.31391200.24412622X-RAY DIFFRACTION100
3.32-3.380.32111330.2322551X-RAY DIFFRACTION100
3.39-3.450.2851370.2232552X-RAY DIFFRACTION100
3.45-3.530.28411620.212543X-RAY DIFFRACTION100
3.53-3.610.23821490.19452561X-RAY DIFFRACTION100
3.61-3.70.22211490.17952540X-RAY DIFFRACTION100
3.7-3.80.28191710.17922511X-RAY DIFFRACTION100
3.8-3.910.20781360.16112578X-RAY DIFFRACTION100
3.91-4.040.18911310.15982580X-RAY DIFFRACTION100
4.04-4.180.17261360.15292571X-RAY DIFFRACTION100
4.19-4.350.18571300.13652542X-RAY DIFFRACTION100
4.35-4.550.17671370.13392594X-RAY DIFFRACTION100
4.55-4.790.21281400.13662538X-RAY DIFFRACTION100
4.79-5.090.17711340.14092570X-RAY DIFFRACTION100
5.09-5.480.27671310.16362580X-RAY DIFFRACTION100
5.48-6.030.22791230.16832578X-RAY DIFFRACTION100
6.03-6.90.22231750.18122509X-RAY DIFFRACTION100
6.9-8.680.17061270.16722588X-RAY DIFFRACTION100
8.7-49.760.18081530.16442526X-RAY DIFFRACTION99

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