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- PDB-5weg: Crystal Structure of UDP-glucose pyrophosphorylase from Sugarcane -

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Basic information

Entry
Database: PDB / ID: 5weg
TitleCrystal Structure of UDP-glucose pyrophosphorylase from Sugarcane
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process
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
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesSaccharum hybrid cultivar SP80-3280 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCotrim, C.A. / Soares, J.S.M. / Kobe, B. / Menossi, M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/06767-3 Brazil
CitationJournal: PLoS ONE / Year: 2018
Title: Crystal structure and insights into the oligomeric state of UDP-glucose pyrophosphorylase from sugarcane.
Authors: Cotrim, C.A. / Soares, J.S.M. / Kobe, B. / Menossi, M.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)105,65413
Polymers104,7002
Non-polymers95511
Water6,359353
1
A: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8247
Polymers52,3501
Non-polymers4746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8306
Polymers52,3501
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.349, 66.789, 74.785
Angle α, β, γ (deg.)75.62, 79.00, 77.52
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 52349.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharum hybrid cultivar SP80-3280 (plant)
Gene: Ugpase-1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A075E2Q1, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES sodium salt, ammonium sulfate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→47.82 Å / Num. obs: 73174 / % possible obs: 97.5 % / Redundancy: 2 % / CC1/2: 0.978 / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.04 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4425 / CC1/2: 0.787 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z90

1z90


Resolution: 2→42.734 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2000 2.73 %
Rwork0.1928 --
obs0.1938 73164 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7065 0 52 353 7470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077228
X-RAY DIFFRACTIONf_angle_d0.8389787
X-RAY DIFFRACTIONf_dihedral_angle_d12.6624390
X-RAY DIFFRACTIONf_chiral_restr0.0541140
X-RAY DIFFRACTIONf_plane_restr0.0051248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.27521390.22774957X-RAY DIFFRACTION95
2.05-2.10550.25841420.21895066X-RAY DIFFRACTION97
2.1055-2.16740.25621430.21435064X-RAY DIFFRACTION97
2.1674-2.23740.23621430.20915082X-RAY DIFFRACTION97
2.2374-2.31730.25271420.19955045X-RAY DIFFRACTION97
2.3173-2.41010.26331420.20245072X-RAY DIFFRACTION97
2.4101-2.51980.25951420.20335077X-RAY DIFFRACTION97
2.5198-2.65260.25731440.20345118X-RAY DIFFRACTION98
2.6526-2.81880.22411430.2085087X-RAY DIFFRACTION98
2.8188-3.03640.26251450.2165139X-RAY DIFFRACTION98
3.0364-3.34180.2341440.20995121X-RAY DIFFRACTION98
3.3418-3.82510.23061430.18945102X-RAY DIFFRACTION98
3.8251-4.81820.18151450.15015143X-RAY DIFFRACTION98
4.8182-42.7440.17541430.16515091X-RAY DIFFRACTION98
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)
12.5986-0.1287-0.61281.21150.29841.13330.0243-0.13480.12730.1249-0.0356-0.05360.00050.1725-0.00550.1608-0.0019-0.04320.11590.07390.106966.518724.826623.7155
21.10570.0138-0.29770.647-0.07990.98440.00370.05380.09440.0274-0.00920.0397-0.0563-0.02870.0090.13570.02150.01130.17310.03090.183862.294825.793816.5627
31.5955-1.52370.27434.5537-1.06780.9848-0.06220.15210.21370.05730.0292-0.0754-0.1040.07520.03210.14570.0218-0.01270.32570.06840.178458.610141.1394-9.6226
43.88031.5386-1.06844.6826-0.19384.9050.27091.1086-0.5369-0.9156-0.10430.16690.2622-0.1313-0.13970.35670.0867-0.05090.4341-0.08070.322539.853761.812114.3616
53.5917-0.6881-0.19272.67480.33531.85070.0521-0.2320.2430.0001-0.0178-0.3315-0.15090.1171-0.05680.1632-0.02820.01330.15420.06450.109558.277.21339.9264
61.47090.16530.19820.76940.06891.85280.0206-0.0472-0.07440.00810.01960.13050.0401-0.2432-0.02450.12480.0374-0.00370.23140.04140.226136.949772.141436.7092
72.8472-0.4907-0.25891.5805-1.31912.4717-0.032-0.1937-0.21790.04130.0456-0.04820.1009-0.1083-0.01450.1275-0.0031-0.01040.20670.03210.157955.378673.45442.4982
82.91190.2397-0.27223.55961.183.6502-0.06990.0153-0.49910.02120.0592-0.12590.43260.15270.03140.1440.0449-0.01810.16140.01020.232263.252459.21431.9338
91.46220.29370.39161.450.30491.93990.04810.0568-0.274-0.0525-0.06710.07560.30150.04430.03080.14620.02630.00880.16250.01570.246651.093865.62230.7367
100.54490.349-0.4680.6691-0.82681.4955-0.0303-0.1925-0.1397-0.0274-0.03160.02770.15510.02290.06640.16710.01470.01990.28450.0710.239544.672457.352956.2067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 368 )
3X-RAY DIFFRACTION3chain 'A' and (resid 369 through 476 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 45 )
5X-RAY DIFFRACTION5chain 'B' and (resid 46 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 227 )
7X-RAY DIFFRACTION7chain 'B' and (resid 228 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 266 through 291 )
9X-RAY DIFFRACTION9chain 'B' and (resid 292 through 336 )
10X-RAY DIFFRACTION10chain 'B' and (resid 337 through 476 )

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