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- PDB-4m28: UDP-Glucose Pyrophosphorylase from Leishmania major in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4m28
TitleUDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp
ComponentsUDP-glucose pyrophosphorylaseUTP—glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UDP-glucose pyrophosphorylase / nucleotidyltransferase / Rossmann-like alpha/beta/alpha sandwich fold
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / nuclear lumen / ciliary plasm / glycogen metabolic process / cytosol / cytoplasm
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-UPC / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFuehring, J.I. / Routier, F.H. / Lamerz, A.-C. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R.
CitationJournal: ACS CATALYSIS / Year: 2013
Title: Catalytic mechanism and allosteric regulation of UDP-glucose pyrophosphorylase from Leishmania major
Authors: Fuehring, J.I. / Routier, F.H. / Lamerz, A.-C. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5212
Polymers56,0551
Non-polymers4661
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-glucose pyrophosphorylase
hetero molecules

A: UDP-glucose pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0424
Polymers112,1102
Non-polymers9322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2950 Å2
ΔGint-10 kcal/mol
Surface area42770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.250, 108.470, 152.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

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Components

#1: Protein UDP-glucose pyrophosphorylase / UTP—glucose-1-phosphate uridylyltransferase


Mass: 56054.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: UGP, LMJF_18_0990 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-UPC / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine


Mass: 466.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M MES, 20% w/v PEG-4000, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2013
Details: monochromator (horizontally side diffracting Silicon 111 crystal).
RadiationMonochromator: monochromator (horizontally side diffracting Silicon 111 crystal).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→47.3 Å / Num. all: 126117 / Num. obs: 11151 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 70 Å2 / Rsym value: 8 / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CNSrefinement
MxCuBEdata collection
XDSdata reduction
SADABSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2OEF

2oef


Resolution: 3→47.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 21.525 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27914 546 4.9 %RANDOM
Rwork0.21326 ---
all0.21642 11151 --
obs0.21642 10539 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.193 Å2
Refinement stepCycle: LAST / Resolution: 3→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 28 76 3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193831
X-RAY DIFFRACTIONr_bond_other_d0.0010.023656
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9775196
X-RAY DIFFRACTIONr_angle_other_deg0.71838435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56924.756164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4915666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6631520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
X-RAY DIFFRACTIONr_mcbond_it5.0058.2881931
X-RAY DIFFRACTIONr_mcbond_other5.0058.2861930
X-RAY DIFFRACTIONr_mcangle_it7.5812.4342412
X-RAY DIFFRACTIONr_mcangle_other7.57812.4362413
X-RAY DIFFRACTIONr_scbond_it5.3828.7361899
X-RAY DIFFRACTIONr_scbond_other5.3498.681887
X-RAY DIFFRACTIONr_scangle_other8.20812.8652764
X-RAY DIFFRACTIONr_long_range_B_refined11.40165.7164259
X-RAY DIFFRACTIONr_long_range_B_other11.29565.6294252
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 46 -
Rwork0.254 713 -
obs--84.52 %

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