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- PDB-6knl: Uridine and triphosphate-bound UGPase from acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 6knl
TitleUridine and triphosphate-bound UGPase from acinetobacter baumannii
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 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
TRIPHOSPHATE / URIDINE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLee, J.H. / Kang, L.W.
CitationJournal: To be published
Title: Uridine and triphosphate-bound UGPase from acinetobacter baumannii
Authors: Kang, L.W.
History
DepositionAug 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5899
Polymers63,3312
Non-polymers1,2597
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-66 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.464, 119.464, 108.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 39 molecules

#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.05 Å3/Da / Density % sol: 59.69 % / Mosaicity: 0.433 °
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: 2.32→50 Å / Num. obs: 34574 / % possible obs: 99.6 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.034 / Rrim(I) all: 0.147 / Χ2: 0.642 / Net I/σ(I): 3.7 / Num. measured all: 490694
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.32-2.367.10.47916980.0640.1860.5160.30299.4
2.36-2.47.90.48416930.0730.1780.5170.33399.6
2.4-2.458.30.47517200.1710.1680.5060.33599.8
2.45-2.58.90.46716680.4040.1590.4950.34699.8
2.5-2.559.20.45617170.2880.1510.4810.33999.7
2.55-2.619.80.43916850.4150.1420.4630.34599.8
2.61-2.6810.30.41917120.6060.1310.4410.3699.6
2.68-2.7510.70.39716950.720.1210.4160.38599.7
2.75-2.8311.40.37417260.7880.1090.3910.40299.7
2.83-2.9211.80.33517010.8870.0960.350.4599.6
2.92-3.0311.80.29617120.9320.0840.3090.43999.5
3.03-3.1515.50.27117250.9610.0670.280.49399.8
3.15-3.2916.80.23117180.9810.0550.2380.57199.8
3.29-3.4718.10.19317200.990.0440.1980.64499.9
3.47-3.6818.90.16417410.9930.0370.1680.70699.9
3.68-3.97200.13817410.9960.030.1410.83799.8
3.97-4.3718.90.11617610.9960.0260.1180.96799.6
4.37-522.90.10117600.9980.020.1030.9999.7
5-6.2922.10.10117940.9980.0210.1030.80799.8
6.29-5021.40.08618870.9980.0180.0880.93398

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-20005.8.0238data scaling
HKL-20003.25data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J49

5j49


Resolution: 2.32→49.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.1853 / FOM work R set: 0.7646 / SU B: 10.826 / SU ML: 0.241 / SU R Cruickshank DPI: 0.2891 / SU Rfree: 0.2444 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 1721 5 %RANDOM
Rwork0.2228 ---
obs0.2256 32805 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.17 Å2 / Biso mean: 39.856 Å2 / Biso min: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.32→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 40 32 4455
Biso mean--113.45 35.53 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134523
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174271
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.6396128
X-RAY DIFFRACTIONr_angle_other_deg1.2481.5739932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.485578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62624.184196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88315779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5671518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
LS refinement shellResolution: 2.32→2.377 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.379 130 -
Rwork0.386 2345 -
obs--98.53 %

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