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- PDB-6ikx: UDP-glucose pyrophosphorylase from acinetobacter baumanii -

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Basic information

Entry
Database: PDB / ID: 6ikx
TitleUDP-glucose pyrophosphorylase from acinetobacter baumanii
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UDP-glucose pyrophosphorylase from acinetobacter baumanii
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
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, J.H. / Kang, L.W.
CitationJournal: To be published
Title: UDP-glucose pyrophosphorylase from acinetobacter baumanii
Authors: Kang, L.W.
History
DepositionOct 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,85419
Polymers63,3312
Non-polymers1,52317
Water1,35175
1
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)129,70838
Polymers126,6624
Non-polymers3,04634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18120 Å2
ΔGint-239 kcal/mol
Surface area45530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.598, 118.598, 108.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 31665.459 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.06 Å3/Da / Density % sol: 59.82 % / Mosaicity: 0.407 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 7.5
Details: 1.5M Ammonium citrate, 0.1M BIS-TRIS pH 6.13 and 0.1M NaCl

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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: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39722 / % possible obs: 99.4 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.029 / Rrim(I) all: 0.112 / Χ2: 2.492 / Net I/σ(I): 10 / Num. measured all: 446063
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.245.50.47819320.0780.2090.5260.90498.4
2.24-2.285.90.4719200.1130.1980.5140.94998.9
2.28-2.326.30.45519540.2040.1850.4950.96798.9
2.32-2.376.90.43519510.3750.1670.469199.1
2.37-2.427.20.41119360.5370.1530.4411.07199.2
2.42-2.4880.37519720.8360.1320.41.12699.6
2.48-2.548.50.36519340.7650.1240.3871.17499.2
2.54-2.619.20.33319700.8560.1080.3511.23299.5
2.61-2.6910.10.29419650.9350.090.3081.37999.8
2.69-2.7710.60.26519840.9660.0780.2771.47499.9
2.77-2.8711.50.23619640.9770.0670.2461.62799.7
2.87-2.9912.70.21119870.9840.0580.2191.85199.8
2.99-3.1213.40.18119870.9910.0480.1872.16299.7
3.12-3.2914.50.15519830.9940.040.162.48699.8
3.29-3.4915.30.12820060.9960.0320.1322.94599.8
3.49-3.7615.60.11619960.9970.0290.123.36799.8
3.76-4.1415.20.10220140.9970.0270.1054.06399.7
4.14-4.7415.10.0920400.9970.0240.0934.31799.7
4.74-5.9715.90.08520540.9980.0220.0883.87999.6
5.97-5015.70.07221730.9980.0190.0743.70798.5

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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: 2.2→47.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.956 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 2062 5.2 %RANDOM
Rwork0.214 ---
obs0.2181 37623 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.02 Å2 / Biso mean: 51.471 Å2 / Biso min: 30.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.2→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 84 75 4487
Biso mean--109.68 51.8 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174225
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6346040
X-RAY DIFFRACTIONr_angle_other_deg1.3131.579823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5315566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72724.184196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26915770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4131518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024858
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02782
LS refinement shellResolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 158 -
Rwork0.441 2681 -
all-2839 -
obs--98.44 %

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