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- PDB-3gue: Crystal Structure of UDP-glucose phosphorylase from Trypanosoma B... -

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Basic information

Entry
Database: PDB / ID: 3gue
TitleCrystal Structure of UDP-glucose phosphorylase from Trypanosoma Brucei, (Tb10.389.0330)
ComponentsUTP-glucose-1-phosphate uridylyltransferase 2
KeywordsTRANSFERASE / TRYPANOSOMA BRUCEI / phosphatase / UDP / glucose / Structural Genomics / Structural Genomics Consortium / SGC / Nucleotidyltransferase
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / nuclear lumen / glycosome / ciliary plasm / glycogen metabolic process / metal ion binding / cytoplasm
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsWernimont, A.K. / Marino, K. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. ...Wernimont, A.K. / Marino, K. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of UDP-glucose phosphorylase from Trypanosoma Brucei, (Tb10.389.0330)
Authors: Wernimont, A.K. / Marino, K. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A. ...Authors: Wernimont, A.K. / Marino, K. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Amani, M.
History
DepositionMar 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 2
B: UTP-glucose-1-phosphate uridylyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,24018
Polymers108,6262
Non-polymers2,61416
Water13,205733
1
A: UTP-glucose-1-phosphate uridylyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5028
Polymers54,3131
Non-polymers1,1897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UTP-glucose-1-phosphate uridylyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,73810
Polymers54,3131
Non-polymers1,4259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.697, 77.485, 112.209
Angle α, β, γ (deg.)90.00, 117.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UTP-glucose-1-phosphate uridylyltransferase 2


Mass: 54313.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.389.0330 / Production host: Escherichia coli (E. coli)
References: UniProt: Q388T4, UTP-glucose-1-phosphate uridylyltransferase

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Non-polymers , 6 types, 749 molecules

#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22% PEG3350, 0.1M Ammonium sulfate, 0.1M Bis Tris, 18% glycerol, 2 mM UDP-glucose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 97362 / Num. obs: 96096 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.096 / Χ2: 1.451 / Net I/σ(I): 10.452
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.33 / Num. unique all: 8757 / Rsym value: 0.645 / Χ2: 0.821 / % possible all: 90.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oeg

2oeg


Resolution: 1.92→25 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.306 / WRfactor Rwork: 0.256 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.794 / SU B: 8.365 / SU ML: 0.144 / SU R Cruickshank DPI: 0.188 / SU Rfree: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 4791 5 %RANDOM
Rwork0.241 ---
all0.243 97332 --
obs0.243 96067 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.26 Å2 / Biso mean: 28.157 Å2 / Biso min: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.45 Å2
2--0.28 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7235 0 158 733 8126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227549
X-RAY DIFFRACTIONr_angle_refined_deg1.5192.00110206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92824.388335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.275151331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5351550
X-RAY DIFFRACTIONr_chiral_restr0.1110.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025573
X-RAY DIFFRACTIONr_nbd_refined0.2030.23682
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2673
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.221
X-RAY DIFFRACTIONr_mcbond_it0.6331.54770
X-RAY DIFFRACTIONr_mcangle_it0.97227442
X-RAY DIFFRACTIONr_scbond_it1.69333112
X-RAY DIFFRACTIONr_scangle_it2.4014.52757
LS refinement shellResolution: 1.918→1.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 298 -
Rwork0.3 5930 -
all-6228 -
obs--87.45 %
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)
14.953-2.22881.59461.0317-0.58711.1047-0.2413-0.0476-0.3140.07470.12740.10450.08940.07120.1139-0.03020.03530.0982-0.1220.03240.092938.6224-19.84355.6097
21.79010.2767-0.2020.814-0.31071.5538-0.06250.173-0.2041-0.16720.0250.10720.2313-0.14430.0375-0.0071-0.0273-0.018-0.0907-0.0253-0.032416.0296-4.70664.4409
34.1606-1.8685-1.19765.2762-0.19463.40490.29260.06340.5352-0.1836-0.1648-0.0535-0.409-0.0978-0.1277-0.0374-0.0486-0.0116-0.1170.0062-0.058228.026813.14476.9623
40.6647-0.8911-0.48233.01661.34831.1090.0086-0.12870.01560.2733-0.0334-0.0874-0.05960.10560.0249-0.0028-0.0022-0.0151-0.02660.0137-0.112433.33725.978914.6035
51.8939-1.1837-1.58941.0240.63731.930.0676-0.2349-0.0819-0.0173-0.1266-0.17010.07090.28720.059-0.0950.03820.0168-0.08140.0314-0.030738.3301-11.70481.5942
62.24880.6523-0.63341.8874-0.17932.64950.0524-0.2590.04470.3043-0.02090.0748-0.0815-0.1299-0.0314-0.06070.01190.0164-0.0649-0.0138-0.110915.4481-1.139313.6279
72.3814-0.80450.72250.9562-0.35364.73740.04980.3358-0.4339-0.1588-0.03540.16580.3104-0.2601-0.0144-0.093-0.05190.01830.0153-0.066-0.048814.4519-8.0455-5.7891
81.9564-0.6829-0.44171.1162-0.39220.7132-0.078-0.0452-0.4169-0.0627-0.04980.05880.10770.01620.1278-0.0461-0.02910.0089-0.0942-0.0014-0.03827.2225-12.88973.419
92.12930.5487-0.6211.7039-0.46715.1894-0.0134-0.0852-0.06650.21520.03970.33540.0234-0.5337-0.0264-0.0573-0.01610.0333-0.05450.0426-0.025116.467710.569-0.3257
104.1228-1.20190.19311.9086-0.16573.32650.02490.2719-0.0722-0.0929-0.00350.0357-0.23860.186-0.0213-0.0165-0.04350.0102-0.0254-0.0038-0.086924.800215.9751-18.913
111.9595-0.2014-0.61841.12310.35340.6943-0.0374-0.20710.38480.01130.0901-0.0291-0.07540.0244-0.0527-0.06680.0031-0.0321-0.04260.0041-0.00361.075517.111545.7537
123.07290.5725-1.66266.3791-2.7614.8264-0.0749-0.3131-0.35220.46630.17910.2074-0.09950.0631-0.1042-0.05210.06510.0671-0.05740.0286-0.13093.768-7.129546.5245
130.88921.1878-0.52716.46460.89614.278-0.08610.30950.3454-0.3917-0.17221.52410.8087-0.9330.25830.1101-0.1606-0.06090.1439-0.06530.1973-5.6036-11.963732.7283
140.4633-0.1826-0.08741.26160.31131.30090.0350.12470.0478-0.06070.0009-0.15750.0690.0655-0.0359-0.0892-0.00660.031-0.08090.0297-0.09847.52964.021539.7713
154.84350.1515-0.35571.22431.20885.4306-0.22440.4953-0.4040.06540.18260.15510.2645-0.52370.0418-0.133-0.07350.02920.0718-0.0084-0.0597-15.76941.409242.3094
162.6001-0.2077-0.55861.1518-0.44693.57650.0099-0.5180.31570.25990.03350.1313-0.5047-0.3114-0.0434-0.02290.0480.0360.0827-0.0552-0.0801-11.469311.410755.8669
172.02620.6650.75591.43910.20661.2584-0.14720.0190.1703-0.04090.02830.0551-0.20750.20540.119-0.0373-0.00460.034-0.0547-0.0065-0.08540.283413.643744.9032
181.5805-0.8051-1.04314.6969-0.46755.6767-0.162-0.0066-0.13780.09070.13480.814-0.1415-0.48720.0272-0.02920.0830.06240.03160.07240.0277-8.5391-5.977551.3792
193.96692.5305-0.18925.6287-0.16244.7611-0.08170.41330.03750.9130.38690.37340.28770.0296-0.30520.21990.17470.0970.07830.0551-0.0591-2.8197-10.964861.7295
200.43361.98950.63869.33762.08524.36770.1794-1.6341-1.23891.37280.2241-0.42220.2101-0.0794-0.40350.47570.0578-0.00560.3073-0.02830.3138-0.8336-16.237873.4546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 56
2X-RAY DIFFRACTION2A57 - 108
3X-RAY DIFFRACTION3A109 - 137
4X-RAY DIFFRACTION4A138 - 181
5X-RAY DIFFRACTION5A182 - 219
6X-RAY DIFFRACTION6A220 - 262
7X-RAY DIFFRACTION7A271 - 324
8X-RAY DIFFRACTION8A325 - 377
9X-RAY DIFFRACTION9A378 - 420
10X-RAY DIFFRACTION10A421 - 483
11X-RAY DIFFRACTION11B26 - 93
12X-RAY DIFFRACTION12B94 - 130
13X-RAY DIFFRACTION13B131 - 145
14X-RAY DIFFRACTION14B146 - 240
15X-RAY DIFFRACTION15B241 - 265
16X-RAY DIFFRACTION16B272 - 322
17X-RAY DIFFRACTION17B323 - 377
18X-RAY DIFFRACTION18B378 - 409
19X-RAY DIFFRACTION19B410 - 462
20X-RAY DIFFRACTION20B463 - 482

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