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- PDB-6mnu: Crystal structure of Yersinia pestis UDP-glucose pyrophosphorylase -

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Basic information

Entry
Database: PDB / ID: 6mnu
TitleCrystal structure of Yersinia pestis UDP-glucose pyrophosphorylase
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UDP-glucose pyrophosphorylase / plague / Yersinia pestis
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Glucose-1-phosphate uridylyltransferase / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.172 Å
AuthorsGibbs, M.E. / Lountos, G.T. / Gumpena, R. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague.
Authors: Gibbs, M.E. / Lountos, G.T. / Gumpena, R. / Waugh, D.S.
History
DepositionOct 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3596
Polymers129,2344
Non-polymers1242
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-87 kcal/mol
Surface area45210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.190, 99.415, 128.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32308.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria)
Gene: galU, galU1, y2631, YP_1428, DBB30_10560, EGT45_14485, NCTC144_03080
Plasmid: pMG3038 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2S9PFH5, UniProt: A0A3N4B738*PLUS, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0 20% PEG Low Smear (PEG 1000, PEG400, PEG600, PEG MME 500), 10 mM spermidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 61347 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Rsym value: 0.08 / Net I/σ(I): 17.1
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3054 / CC1/2: 0.774 / Rpim(I) all: 0.343 / Rrim(I) all: 0.722 / Rsym value: 0.631 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3D

2e3d


Resolution: 2.172→26.709 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.38
RfactorNum. reflection% reflection
Rfree0.2409 1997 3.26 %
Rwork0.1767 --
obs0.1787 61296 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.172→26.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8665 0 8 623 9296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088843
X-RAY DIFFRACTIONf_angle_d0.91211999
X-RAY DIFFRACTIONf_dihedral_angle_d2.8436448
X-RAY DIFFRACTIONf_chiral_restr0.0521432
X-RAY DIFFRACTIONf_plane_restr0.0061533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1724-2.22670.33221480.22664053X-RAY DIFFRACTION95
2.2267-2.28690.29831360.21284252X-RAY DIFFRACTION99
2.2869-2.35420.29691450.20914251X-RAY DIFFRACTION99
2.3542-2.43010.24761430.19824277X-RAY DIFFRACTION99
2.4301-2.51690.28721450.19094198X-RAY DIFFRACTION98
2.5169-2.61760.24621440.19344208X-RAY DIFFRACTION98
2.6176-2.73660.28821360.19774218X-RAY DIFFRACTION98
2.7366-2.88070.24771440.19554237X-RAY DIFFRACTION98
2.8807-3.0610.27261350.20254241X-RAY DIFFRACTION98
3.061-3.29690.30211390.19964260X-RAY DIFFRACTION98
3.2969-3.6280.22651440.17564260X-RAY DIFFRACTION98
3.628-4.15130.20461470.15474251X-RAY DIFFRACTION97
4.1513-5.22370.22351420.14124259X-RAY DIFFRACTION96
5.2237-26.71110.17821490.15464334X-RAY DIFFRACTION94

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