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- PDB-6k8d: UDP-glucose pyrophosphorylase with UPG from Acinetobacter Baumanii -

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Basic information

Entry
Database: PDB / ID: 6k8d
TitleUDP-glucose pyrophosphorylase with UPG from Acinetobacter Baumanii
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UGPase / Rossman fold
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-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
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsLee, J.H. / Kang, L.W.
CitationJournal: To be published
Title: UDP-glucose pyrophosphorylase with UPG from Acinetobacter Baumanii
Authors: Kang, L.W.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,75417
Polymers126,6624
Non-polymers3,09213
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17880 Å2
ΔGint-195 kcal/mol
Surface area43970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.525, 114.382, 114.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 31665.459 Da / Num. of mol.: 4 / Mutation: Q286L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: galU, B9X91_19205, CBI29_00108, CSB70_3798, DVA79_14980
Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: X2KZJ9, UTP-glucose-1-phosphate uridylyltransferase

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Non-polymers , 5 types, 19 molecules

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


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.88 Å3/Da / Density % sol: 57.27 % / Mosaicity: 0.494 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 7.5
Details: 0.5M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5 and 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 30489 / % possible obs: 97.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.047 / Rrim(I) all: 0.113 / Χ2: 1.811 / Net I/σ(I): 8.6 / Num. measured all: 142270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-32.70.38914140.0870.2610.4720.78392.1
3-3.062.80.37314490.1910.2440.4490.77793.2
3.06-3.113.10.36814240.2230.2290.4370.83392.5
3.11-3.183.20.34214630.3210.2060.4020.8594
3.18-3.253.40.32914580.6020.1920.3830.95395.4
3.25-3.323.70.28915050.6970.160.3321.01795.9
3.32-3.413.90.25414400.8330.1350.2891.08196.2
3.41-3.54.10.23715260.8740.1240.2691.15696.9
3.5-3.64.30.2215220.9040.110.2471.30797.6
3.6-3.724.60.19615400.930.0960.2191.39597.7
3.72-3.854.80.17815190.9550.0840.1971.73498.4
3.85-45.10.16215450.9680.0750.1791.96999.1
4-4.195.30.13715460.9830.0620.1512.28699
4.19-4.415.50.12515540.9860.0560.1372.48198.5
4.41-4.685.90.10315380.990.0450.1122.69699.3
4.68-5.045.90.09515860.9910.0410.1042.47399.5
5.04-5.555.90.08715760.9930.0380.0952.07899.2
5.55-6.355.80.08515820.9940.0360.0921.87298.6
6.35-86.20.06716190.9970.0280.0731.98199.3
8-506.40.05216830.9970.0220.0572.27198.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J49

5j49


Resolution: 2.94→40.47 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / SU B: 25.261 / SU ML: 0.447 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.467
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 1479 4.9 %RANDOM
Rwork0.2183 ---
obs0.2216 28986 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.99 Å2 / Biso mean: 66.434 Å2 / Biso min: 36.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.94→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8642 0 189 6 8837
Biso mean--74.11 43.11 -
Num. residues----1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138971
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178394
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.63812207
X-RAY DIFFRACTIONr_angle_other_deg1.1491.56919494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.16351154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3524.194372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.212151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4351533
X-RAY DIFFRACTIONr_chiral_restr0.0550.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029836
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021583
LS refinement shellResolution: 2.941→3.017 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 88 -
Rwork0.378 1914 -
all-2002 -
obs--88.51 %

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