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- PDB-8x7s: Crystal structure of tlr0611 -

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Basic information

Entry
Database: PDB / ID: 8x7s
TitleCrystal structure of tlr0611
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Crystal structure of tlr0611
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 / UTP binding / magnesium ion binding
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, cyanobacteria / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesThermosynechococcus vestitus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSu, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of tlr0611
Authors: Su, J.Y.
History
DepositionNov 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: UTP--glucose-1-phosphate uridylyltransferase
A: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)133,0913
Polymers133,0913
Non-polymers00
Water00
1
B: UTP--glucose-1-phosphate uridylyltransferase
A: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase
A: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)266,1826
Polymers266,1826
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area22070 Å2
ΔGint-81 kcal/mol
Surface area88880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.304, 99.304, 310.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UTP--glucose-1-phosphate uridylyltransferase


Mass: 44363.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1) (bacteria)
Gene: cugP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DL85
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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.35→19.86 Å / Num. obs: 23126 / % possible obs: 99.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 3.35→3.62 Å / Rmerge(I) obs: 0.964 / Num. unique obs: 4680

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→19.86 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 1999 8.67 %
Rwork0.254 --
obs0.2559 23054 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 0 0 9030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039243
X-RAY DIFFRACTIONf_angle_d0.67712553
X-RAY DIFFRACTIONf_dihedral_angle_d10.8241246
X-RAY DIFFRACTIONf_chiral_restr0.0521418
X-RAY DIFFRACTIONf_plane_restr0.0051617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.430.40491390.38211476X-RAY DIFFRACTION100
3.43-3.530.36911400.36531462X-RAY DIFFRACTION100
3.53-3.630.42341380.35851458X-RAY DIFFRACTION100
3.63-3.750.34891390.3441476X-RAY DIFFRACTION99
3.75-3.880.34271420.33151484X-RAY DIFFRACTION100
3.88-4.030.31351410.29781480X-RAY DIFFRACTION100
4.03-4.210.31151400.28881485X-RAY DIFFRACTION100
4.21-4.430.30231430.27381498X-RAY DIFFRACTION100
4.43-4.710.27881440.24781517X-RAY DIFFRACTION100
4.71-5.070.25771410.24091486X-RAY DIFFRACTION100
5.07-5.570.2771440.25461519X-RAY DIFFRACTION100
5.57-6.350.32361450.26561527X-RAY DIFFRACTION99
6.35-7.910.24441480.24141557X-RAY DIFFRACTION100
7.92-19.860.19111550.17341630X-RAY DIFFRACTION98

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