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

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Basic information

Entry
Database: PDB / ID: 6ikz
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
PYROPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLee, J.H. / Kang, L.W.
CitationJournal: To be published
Title: UTP-bound UGPase 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)64,66211
Polymers63,3312
Non-polymers1,3319
Water1448
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)129,32322
Polymers126,6624
Non-polymers2,66118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area17530 Å2
ΔGint-234 kcal/mol
Surface area45480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.025, 119.025, 108.244
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, 17 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.01 Å3/Da / Density % sol: 59.19 % / Mosaicity: 0.547 °
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: 2.14→50 Å / Num. obs: 42093 / % possible obs: 97.8 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.026 / Rrim(I) all: 0.097 / Χ2: 3.258 / Net I/σ(I): 15 / Num. measured all: 499943
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.185.90.49120830.3580.2090.5361.30798.8
2.18-2.225.90.44820770.360.1890.4891.31998.4
2.22-2.266.70.46720240.5180.1760.5033.2296
2.26-2.3160.38720140.650.160.4221.47295.6
2.31-2.367.90.36721200.8510.1330.3931.57499.2
2.36-2.418.80.32521170.9160.110.3451.64399.3
2.41-2.479.60.28621160.9610.0920.3021.76899.4
2.47-2.5410.30.26620960.9840.0820.2791.80899.6
2.54-2.6111.30.23821300.9790.070.2481.98699.6
2.61-2.712.40.20521360.9880.0570.2132.18999.9
2.7-2.7913.20.18121070.9930.0490.1872.3699.9
2.79-2.914.40.15621350.9950.040.1612.61999.9
2.9-3.0415.60.13821500.9960.0350.1423.01299.8
3.04-3.216.50.11821490.9970.0290.1223.44999.8
3.2-3.417.10.10421540.9980.0250.1074.03499.9
3.4-3.6615.90.09321550.9970.0240.0964.51499.7
3.66-4.0314.40.08221490.9960.0230.0864.99398.6
4.03-4.6114.40.07520480.9960.0210.0785.15193.6
4.61-5.8115.20.07121090.9960.0190.0744.96594.5
5.81-5015.20.06620240.9960.0170.0684.69885.1

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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: 2.33→37.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.946 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.266
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2979 1667 5 %RANDOM
Rwork0.2323 ---
obs0.2357 31448 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 239.57 Å2 / Biso mean: 56.089 Å2 / Biso min: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.33→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4318 0 74 8 4400
Biso mean--133.79 47.89 -
Num. residues----575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134450
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174164
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6366035
X-RAY DIFFRACTIONr_angle_other_deg1.2711.5719659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9525572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54824.062192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13715750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.611518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024873
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02791
LS refinement shellResolution: 2.331→2.391 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 106 -
Rwork0.463 2064 -
all-2170 -
obs--89.41 %

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