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- PDB-4m2b: Crystal structure of L281D mutant of udp-glucose pyrophosphorylas... -

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Basic information

Entry
Database: PDB / ID: 4m2b
TitleCrystal structure of L281D mutant of udp-glucose pyrophosphorylase from leishmania major in complex with udp-glc
ComponentsUDP-glucose pyrophosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / ciliary plasm / nuclear lumen / glycogen metabolic process / cytoplasm / cytosol
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
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFuehring, J. / 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. / 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 1.1Feb 19, 2014Group: Database references
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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)56,6232
Polymers56,0571
Non-polymers5661
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.790, 86.900, 138.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein UDP-glucose pyrophosphorylase


Mass: 56056.699 Da / Num. of mol.: 1 / Mutation: L281D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_18_0990, UGP / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 277 K / pH: 6.6
Details: 0.1M BIS-TRIS, 28% W/V PEG-MME -2000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K, pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.816
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 25, 2006
RadiationMonochromator: A SINGLE GE(111) TRIANGULAR BENT CRYSTAL. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.816 Å / Relative weight: 1
ReflectionResolution: 2.2→23.4 Å / Num. obs: 23985 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.076 / Net I/σ(I): 14.4

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Processing

Software
NameClassification
MxCuBEdata collection
CCP4model building
REFMACrefinement
XDSdata reduction
SADABSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OEG

2oeg


Resolution: 2.2→23.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.242 1204 RANDOM
Rwork0.175 --
obs0.178 23985 -
all-23985 -
Displacement parametersBiso mean: 29.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 36 393 4159

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