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- PDB-8f73: Crystal structure of Pseudomonas aeruginosa UDP-glucose phosphory... -

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Basic information

Entry
Database: PDB / ID: 8f73
TitleCrystal structure of Pseudomonas aeruginosa UDP-glucose phosphorylase in complex with UDP-glucose
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UGP / UDP-Glucose pyrophosphorylase / UTP:glucose-1-phosphate uridylyltransferase
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / lipopolysaccharide core region biosynthetic process
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDirr, L. / Fuehring, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1157150 Australia
CitationJournal: To Be Published
Title: Crystal structure of Pseudomonas aeruginosa UDP-glucose phosphorylase in complex with UDP-glucose
Authors: Dirr, L. / Fuehring, J.
History
DepositionNov 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: UTP--glucose-1-phosphate uridylyltransferase
F: UTP--glucose-1-phosphate uridylyltransferase
G: UTP--glucose-1-phosphate uridylyltransferase
H: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,56828
Polymers254,5978
Non-polymers4,97020
Water1,838102
1
A: UTP--glucose-1-phosphate uridylyltransferase
H: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

F: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,78214
Polymers127,2994
Non-polymers2,48410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area15860 Å2
ΔGint-111 kcal/mol
Surface area41580 Å2
MethodPISA
2
C: UTP--glucose-1-phosphate uridylyltransferase
G: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

D: UTP--glucose-1-phosphate uridylyltransferase
E: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,78514
Polymers127,2994
Non-polymers2,48710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area15870 Å2
ΔGint-105 kcal/mol
Surface area41640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.715, 114.847, 155.761
Angle α, β, γ (deg.)90.000, 97.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
UTP--glucose-1-phosphate uridylyltransferase / Alpha-D-glucosyl-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Uridine ...Alpha-D-glucosyl-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Uridine diphosphoglucose pyrophosphorylase


Mass: 31824.680 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: galU, PA2023 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9I291, UTP-glucose-1-phosphate uridylyltransferase

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Non-polymers , 5 types, 122 molecules

#2: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate pH 4.6 2.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953722 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953722 Å / Relative weight: 1
ReflectionResolution: 2.9→48.52 Å / Num. obs: 65768 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 60.43 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.3
Reflection shellResolution: 2.9→2.97 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4608 / CC1/2: 1 / Rpim(I) all: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUK

3juk


Resolution: 2.9→46.98 Å / SU ML: 0.3435 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 3227 4.93 %
Rwork0.1948 62216 -
obs0.1968 65443 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 312 102 17670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007317881
X-RAY DIFFRACTIONf_angle_d0.996924178
X-RAY DIFFRACTIONf_chiral_restr0.05882736
X-RAY DIFFRACTIONf_plane_restr0.0053096
X-RAY DIFFRACTIONf_dihedral_angle_d16.44766930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.33181490.29192704X-RAY DIFFRACTION99.55
2.94-2.990.3151490.29482660X-RAY DIFFRACTION99.75
2.99-3.040.32531470.27522691X-RAY DIFFRACTION99.44
3.04-3.090.33981370.26612687X-RAY DIFFRACTION99.47
3.09-3.150.28751360.25432685X-RAY DIFFRACTION99.61
3.15-3.210.29421320.25192678X-RAY DIFFRACTION99.12
3.21-3.270.31461250.24792737X-RAY DIFFRACTION99.44
3.27-3.340.30581520.23912652X-RAY DIFFRACTION99.19
3.34-3.420.2721390.23532713X-RAY DIFFRACTION99.58
3.42-3.510.26161280.21172695X-RAY DIFFRACTION99.82
3.51-3.60.27511440.19922697X-RAY DIFFRACTION99.79
3.6-3.710.25121430.18722714X-RAY DIFFRACTION99.58
3.71-3.830.21291470.18772696X-RAY DIFFRACTION99.82
3.83-3.960.22441520.18372685X-RAY DIFFRACTION99.75
3.96-4.120.26441380.18162702X-RAY DIFFRACTION99.75
4.12-4.310.19541370.16792734X-RAY DIFFRACTION99.86
4.31-4.540.20631290.15252703X-RAY DIFFRACTION99.65
4.54-4.820.20171360.14642718X-RAY DIFFRACTION99.86
4.82-5.190.18081400.15412738X-RAY DIFFRACTION99.69
5.19-5.720.19321400.17892724X-RAY DIFFRACTION99.69
5.72-6.540.23751440.21132723X-RAY DIFFRACTION99.76
6.54-8.230.22291570.20132713X-RAY DIFFRACTION99.41
8.23-46.980.18811260.17642767X-RAY DIFFRACTION97.8

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