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- PDB-8b6d: Crystal structure of UDP-glucose pyrophosphorylase from Thermocri... -

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Basic information

Entry
Database: PDB / ID: 8b6d
TitleCrystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070 in complex with UDP
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / sugar metabolism / Mg2+ / GalU / UTP / glucose 1-phosphate / pyrimidine nucleosides.
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'-DIPHOSPHATE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesThermocrispum agreste DSM 44070 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLaustsen, J. / Kumpf, A. / Bento, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)100263899European Union
CitationJournal: To Be Published
Title: Crystal structure determination of a highly active UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070
Authors: Kumpf, A. / Maier, A. / Laustsen, J.U. / Jeffries, C.M. / Bento, I. / Tischler, D.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: 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)65,45910
Polymers64,2272
Non-polymers1,2328
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-51 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.752, 65.752, 329.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32113.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum agreste DSM 44070 (bacteria)
Gene: DIU77_00305 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2W4LV58, UTP-glucose-1-phosphate uridylyltransferase

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 5.5 / Details: sodium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→82.53 Å / Num. obs: 43788 / % possible obs: 100 % / Redundancy: 26.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.024 / Rrim(I) all: 0.093 / Net I/σ(I): 29.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 26.9 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 3.86 / Num. unique obs: 4253 / CC1/2: 1 / CC star: 0.98 / Rpim(I) all: 0.24 / Rrim(I) all: 1.28

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
Aimlessdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-TaGalU

Resolution: 2.1→82.524 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.394 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2209 2094 4.795 %
Rwork0.1748 41581 -
all0.177 --
obs-43675 99.918 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.301 Å2
Baniso -1Baniso -2Baniso -3
1-1.638 Å20 Å20 Å2
2--1.638 Å20 Å2
3----3.277 Å2
Refinement stepCycle: LAST / Resolution: 2.1→82.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 77 264 4745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164351
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6556345
X-RAY DIFFRACTIONr_angle_other_deg0.5761.56310146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.227541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25510732
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.8910201
X-RAY DIFFRACTIONr_chiral_restr0.080.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined0.2210.2930
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.23947
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22246
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.214
X-RAY DIFFRACTIONr_nbd_other0.1880.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.217
X-RAY DIFFRACTIONr_mcbond_it2.9632.7142358
X-RAY DIFFRACTIONr_mcbond_other2.9542.7142358
X-RAY DIFFRACTIONr_mcangle_it4.1274.0552954
X-RAY DIFFRACTIONr_mcangle_other4.1274.0562955
X-RAY DIFFRACTIONr_scbond_it4.1333.1952286
X-RAY DIFFRACTIONr_scbond_other4.1323.1962287
X-RAY DIFFRACTIONr_scangle_it6.1574.6193385
X-RAY DIFFRACTIONr_scangle_other6.1564.623386
X-RAY DIFFRACTIONr_lrange_it8.53255.2519235
X-RAY DIFFRACTIONr_lrange_other8.50854.58119067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.2581470.23129870.23231460.9490.96199.61860.206
2.154-2.2130.2911470.22829390.23130910.9410.96399.83820.201
2.213-2.2780.2861450.21628440.21929940.9460.96899.8330.19
2.278-2.3480.2141440.18527860.18729330.970.97899.89770.158
2.348-2.4250.2291310.19126800.19328130.9680.97799.92890.166
2.425-2.510.2461200.19726230.19927440.9640.97699.96360.176
2.51-2.6040.2411430.18525010.18826450.9640.9899.96220.163
2.604-2.710.2381070.19424470.19625540.9630.9781000.167
2.71-2.8310.2631190.223500.20324690.9550.9761000.173
2.831-2.9690.2651380.1922220.19423600.9540.9791000.166
2.969-3.1290.2461010.19821720.222730.9610.9751000.177
3.129-3.3190.253940.18520370.18821330.9630.9899.90620.17
3.319-3.5470.204960.17219030.17419990.9750.9851000.163
3.547-3.8310.25790.18418260.18619050.9620.9821000.175
3.831-4.1960.174900.1616640.16117540.9810.9851000.155
4.196-4.690.145840.12715390.12816230.990.9911000.126
4.69-5.4120.139600.13213590.13214190.9870.9911000.131
5.412-6.6210.254700.17711760.18112470.970.98599.91980.174
6.621-9.3340.189480.1459490.1479970.9780.9881000.154
9.334-82.5240.327310.1835770.1896090.9390.97499.83580.195
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)
10.89620.20610.71430.7058-0.03122.928-0.0143-0.0868-0.043-0.0599-0.0306-0.03440.02680.01390.04490.04640.0314-0.01090.0827-0.01010.132921.55830.2302-12.5082
20.96590.28680.90490.99940.36833.43060.0625-0.102-0.06780.0502-0.06590.09660.1994-0.16970.00340.01690.01280.01180.14890.04560.16636.7043-2.371919.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLALLA9 - 299
2X-RAY DIFFRACTION1ALLALLB9 - 299

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