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- PDB-9ygk: Crystal Structure UTP--glucose-1-phosphate uridylyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 9ygk
TitleCrystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound)
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyUTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / Nucleotidyl transferase domain / Nucleotidyl transferase / biosynthetic process / Nucleotide-diphospho-sugar transferases / UTP--glucose-1-phosphate uridylyltransferase
Function and homology information
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionSep 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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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)64,19127
Polymers61,9832
Non-polymers2,20825
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-212 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.246, 95.799, 81.205
Angle α, β, γ (deg.)90.00, 110.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-413-

CL

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Components

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


Mass: 30991.625 Da / Num. of mol.: 2 / Fragment: 26-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: BP3403 / Plasmid: BopeA.00118.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7VTV0, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Index B6: 0.1M HEPES pH 7.0, 1.4M Sodium citrate tribasic dihydrate. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate 19780 B6 drop 1, Puck: PSL-1201, Cryo: 2.5M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 7, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→47.16 Å / Num. obs: 58027 / % possible obs: 95.6 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Χ2: 0.83 / Net I/σ(I): 14 / Num. measured all: 400715
Reflection shellResolution: 1.95→2 Å / % possible obs: 98.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.004 / Num. measured all: 29919 / Num. unique obs: 4194 / CC1/2: 0.833 / Rpim(I) all: 0.401 / Rrim(I) all: 1.082 / Χ2: 0.7 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5819: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.16 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 2895 4.99 %
Rwork0.1843 --
obs0.1862 57968 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 116 229 4448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184293
X-RAY DIFFRACTIONf_angle_d1.2895856
X-RAY DIFFRACTIONf_dihedral_angle_d13.131557
X-RAY DIFFRACTIONf_chiral_restr0.087680
X-RAY DIFFRACTIONf_plane_restr0.012749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.30511320.25332751X-RAY DIFFRACTION98
1.98-2.020.28331350.23622664X-RAY DIFFRACTION98
2.02-2.050.31011440.23322650X-RAY DIFFRACTION98
2.05-2.090.2751530.23652529X-RAY DIFFRACTION91
2.09-2.130.28911390.22852646X-RAY DIFFRACTION98
2.14-2.180.29891620.22142679X-RAY DIFFRACTION98
2.18-2.230.26281490.20712677X-RAY DIFFRACTION99
2.23-2.290.27331390.20022513X-RAY DIFFRACTION91
2.29-2.350.24121340.18822693X-RAY DIFFRACTION99
2.35-2.420.23661480.18682721X-RAY DIFFRACTION99
2.42-2.50.24681460.1872678X-RAY DIFFRACTION99
2.5-2.590.25471310.19882731X-RAY DIFFRACTION99
2.59-2.690.2982970.21642088X-RAY DIFFRACTION75
2.69-2.810.25871500.21892707X-RAY DIFFRACTION99
2.81-2.960.26791140.21892777X-RAY DIFFRACTION99
2.96-3.150.27161310.22362757X-RAY DIFFRACTION99
3.15-3.390.24931400.20832738X-RAY DIFFRACTION100
3.39-3.730.18241130.16371986X-RAY DIFFRACTION73
3.73-4.270.19211480.14982511X-RAY DIFFRACTION91
4.27-5.380.15511500.13322755X-RAY DIFFRACTION99
5.38-47.160.20861400.17952822X-RAY DIFFRACTION100
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)
17.8212-3.20610.68792.57850.20691.23990.1793-0.1420.2695-0.0492-0.09980.0503-0.11530.0602-0.07330.4614-0.01130.0390.31070.03030.3458-1.34560.813524.8356
23.73361.49370.53651.49990.61093.99260.1496-0.1949-0.2360.1638-0.14110.09060.2714-0.22740.00160.3980.0393-0.00260.28740.02130.3491-1.3944-7.467126.4951
31.63880.42850.33324.5088-0.85993.9821-0.00370.06710.06370.0996-0.01520.1136-0.08530.22090.01740.271-0.01640.01270.4123-0.02630.3413.84218.095215.8986
48.45541.7675-0.54362.105-0.10080.24940.25470.5737-0.4015-0.0609-0.0590.03-0.01930.0078-0.1820.38140.0689-0.00050.4533-0.02440.2597-0.9852-2.63189.1456
53.64952.6302-1.18612.5050.14271.97560.1102-0.0999-0.50330.0569-0.1429-0.13750.02640.06180.04210.43310.0204-0.0430.27690.07130.3534-1.1268-8.925551.1661
63.6031-0.739-1.16711.70720.67112.34590.05180.0035-0.1164-0.0192-0.14510.05860.0655-0.10650.09690.4223-0.003-0.03460.32210.02890.372-2.7237-2.129950.7436
72.3209-1.41980.41221.9534-0.97523.23840.0387-0.04790.16830.00890.0608-0.0318-0.2817-0.0856-0.09880.3258-0.0322-0.00230.2663-0.00580.35313.9253-3.519753.0501
82.2341.359-0.65512.977-0.13832.4685-0.1465-0.2866-0.10580.2917-0.1898-0.243-0.01610.26020.2510.38180.0594-0.03420.55960.03620.462616.0991-19.392265.7367
90.254-0.7550.32723.3903-0.53011.3238-0.1288-0.3106-0.03380.41660.07880.0036-0.10860.07470.10440.38510.0416-0.07520.50330.03360.434211.9957-14.13460.9635
109.5271-1.11730.66972.3824-4.32768.38270.44150.1269-0.6988-0.396-0.303-0.51681.46980.7334-0.18280.63280.0885-0.08480.3747-0.02690.542315.4908-19.774148.5008
116.9559-2.09810.06381.91360.28050.23140.1984-0.4876-0.03290.15060.0231-0.08760.15340.0412-0.20880.4304-0.0415-0.05260.44120.05480.31990.6301-5.778766.3329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 264 )
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 302 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 49 )
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 91 )
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 194 )
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 220 )
9X-RAY DIFFRACTION9chain 'B' and (resid 221 through 234 )
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 263 )
11X-RAY DIFFRACTION11chain 'B' and (resid 264 through 302 )

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