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- PDB-8b31: Crystal structure of UDP-glucose pyrophosphorylase from Thermocri... -

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Basic information

Entry
Database: PDB / ID: 8b31
TitleCrystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Glycosyl transferase / UDP-glucose pyrophosphorylase / sugar metabolism
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
: / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesThermocrispum agreste DSM 44070 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLaustsen, J.U. / 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 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: 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)65,74326
Polymers64,2592
Non-polymers1,48424
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint29 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.086, 78.593, 89.788
Angle α, β, γ (deg.)90.000, 93.885, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32129.451 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, 441 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 6.5 / Details: Bis-Tris-Propane, PEG3350, KSCN, Ethylene Glycol

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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: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.75→89.58 Å / Num. obs: 67139 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.035 / Rrim(I) all: 0.069 / Net I/σ(I): 10.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3700 / CC1/2: 0.651 / Rpim(I) all: 0.541 / Rrim(I) all: 1.025 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUJ

3juj


Resolution: 1.75→48.022 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.599 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2262 3270 4.873 %
Rwork0.196 63838 -
all0.198 --
obs-67108 99.761 %
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: 32.816 Å2
Baniso -1Baniso -2Baniso -3
1-2.122 Å2-0 Å2-1.419 Å2
2---0.948 Å2-0 Å2
3----0.972 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 92 417 4893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124597
X-RAY DIFFRACTIONr_bond_other_d0.0060.0164398
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.6636220
X-RAY DIFFRACTIONr_angle_other_deg0.6391.56210234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.216542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08410731
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg18.407103
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.86610199
X-RAY DIFFRACTIONr_chiral_restr0.0880.2712
X-RAY DIFFRACTIONr_chiral_restr_other0.0490.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025257
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02827
X-RAY DIFFRACTIONr_nbd_refined0.2080.2906
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.24103
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22179
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2374
X-RAY DIFFRACTIONr_metal_ion_refined0.3040.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.216
X-RAY DIFFRACTIONr_nbd_other0.1760.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.29
X-RAY DIFFRACTIONr_mcbond_it2.1132.2982322
X-RAY DIFFRACTIONr_mcbond_other2.1132.2972321
X-RAY DIFFRACTIONr_mcangle_it3.063.4292899
X-RAY DIFFRACTIONr_mcangle_other3.063.4292900
X-RAY DIFFRACTIONr_scbond_it2.9192.6522275
X-RAY DIFFRACTIONr_scbond_other2.9192.6522276
X-RAY DIFFRACTIONr_scangle_it4.3413.8323315
X-RAY DIFFRACTIONr_scangle_other4.343.8333316
X-RAY DIFFRACTIONr_lrange_it7.07346.42919323
X-RAY DIFFRACTIONr_lrange_other6.95945.76818956
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
1.75-1.7950.3342350.34246960.34249500.9120.90699.61620.328
1.795-1.8450.32240.29646230.29648550.930.93199.83520.274
1.845-1.8980.332180.26444210.26746480.920.94999.80640.241
1.898-1.9560.261910.25343640.25345660.9480.95599.75910.229
1.956-2.020.2172220.22342000.22344250.9640.96699.93220.201
2.02-2.0910.272140.21240690.21443030.9590.96999.53520.192
2.091-2.170.2182150.19738500.19840770.970.97499.70570.179
2.17-2.2580.242160.19737970.19940160.960.97599.92530.181
2.258-2.3580.2481910.235750.20237790.9570.97599.6560.183
2.358-2.4730.2181700.18634840.18836620.9680.97899.78150.174
2.473-2.6070.2361620.19332930.19534600.9670.97799.85550.183
2.607-2.7640.2261680.18831340.1933040.9670.97799.93950.181
2.764-2.9540.2431670.19929050.20130730.9630.97599.96750.197
2.954-3.190.2181340.19927770.229130.9690.97799.93130.203
3.19-3.4930.2031390.18825000.18926480.9770.98299.66010.194
3.493-3.9030.2241040.17922860.18124010.9720.98299.54190.19
3.903-4.5020.173910.16320260.16321260.9840.98599.57670.183
4.502-5.5010.2011040.16117170.16318250.9780.98699.78080.181
5.501-7.7290.253690.21113330.21314080.9620.97799.57390.241
7.729-48.0220.214360.1837880.1848280.9640.97599.51690.21
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)
10.4066-0.09430.02811.95571.07941.81160.0106-0.04960.05790.0610.0101-0.16480.04850.135-0.02070.00250.0004-0.00280.03790.00590.0253-17.6589-1.391233.094
20.380.1882-0.00091.02141.21822.13940.01460.1369-0.0432-0.04490.1307-0.17230.13060.2127-0.14530.13260.04780.00180.0863-0.01210.0439-16.0276-30.236312.8602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLALLA9 - 299
2X-RAY DIFFRACTION1ALLB9 - 299

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