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- PDB-6knj: UTP-bound UGPase from acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 6knj
TitleUTP-bound UGPase from acinetobacter baumannii
Components(UTP--glucose-1-phosphate ...) x 2
KeywordsTRANSFERASE / UGPase / Rossman fold
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-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
URIDINE 5'-TRIPHOSPHATE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLee, J.H. / Kang, L.W.
CitationJournal: To be published
Title: UTP-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)64,5196
Polymers63,3632
Non-polymers1,1564
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-60 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.376, 117.376, 110.275
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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UTP--glucose-1-phosphate ... , 2 types, 2 molecules AB

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


Mass: 31697.459 Da / Num. of mol.: 1
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: Protein UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase


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

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Non-polymers , 4 types, 6 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
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: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 32126 / % possible obs: 97.4 % / Redundancy: 6.7 % / Rpim(I) all: 0.05 / Net I/σ(I): 9.4
Reflection shellResolution: 3.2→3.283 Å / Rmerge(I) obs: 0.459 / Num. unique obs: 13108

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Processing

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

5j49


Resolution: 3.2→49.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / SU B: 70.4 / SU ML: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.561
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 625 4.8 %RANDOM
Rwork0.2159 ---
obs0.2193 12483 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.14 Å2 / Biso mean: 51.955 Å2 / Biso min: 26.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å2-0 Å2
2--0.82 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 3.2→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 69 2 4301
Biso mean--97.08 56.11 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134362
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174070
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.6365920
X-RAY DIFFRACTIONr_angle_other_deg1.3241.579426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3135566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26124.045178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.84815712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3961516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024787
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02780
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 41 -
Rwork0.408 893 -
all-934 -
obs--97.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0044-0.2279-1.2061.65950.01281.6480.10730.09610.01980.2504-0.00440.5791-0.2151-0.495-0.10290.30380.23630.03880.4044-0.02530.226-27.36047.824-15.4636
21.84180.173-0.58443.43860.7542.1168-0.13760.2065-0.48620.07180.11540.12950.3971-0.28380.02210.18030.0334-0.05310.1419-0.07880.187-6.2443-19.194-24.0138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 289
2X-RAY DIFFRACTION2B0 - 289

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