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- PDB-1vst: Symmetric Sulfolobus solfataricus uracil phosphoribosyltransferas... -

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Basic information

Entry
Database: PDB / ID: 1vst
TitleSymmetric Sulfolobus solfataricus uracil phosphoribosyltransferase with bound PRPP and GTP
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / uracil / phosphoribosyltransferase / allosteric regulation / Sulfolobus solfataricus / PRPP / GTP / Glycosyltransferase / Magnesium
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / UMP salvage / GMP salvage / IMP salvage / GTP binding ...uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / UMP salvage / GMP salvage / IMP salvage / GTP binding / magnesium ion binding / cytosol
Similarity search - Function
Uracil phosphoribosyltransferase, archaea / Uracil phosphoribosyl transferase / Uracil phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Chem-PRP / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKadziola, A.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus
Authors: Christoffersen, S. / Kadziola, A. / Johansson, E. / Rasmussen, M. / Willemoes, M. / Jensen, K.F.
#1: Journal: Biochemistry / Year: 2005
Title: Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus.
Authors: Arent, S. / Harris, P. / Jensen, K.F. / Larsen, S.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1174
Polymers24,1791
Non-polymers9383
Water18010
1
A: Uracil phosphoribosyltransferase
hetero molecules

A: Uracil phosphoribosyltransferase
hetero molecules

A: Uracil phosphoribosyltransferase
hetero molecules

A: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46816
Polymers96,7174
Non-polymers3,75012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area17040 Å2
ΔGint-160 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.2, 122.2, 62.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-302-

MG

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Components

#1: Protein Uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 24179.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0231, upp / Plasmid: pLFS2 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830
References: UniProt: Q980Q4, uracil phosphoribosyltransferase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG8000, 0.1M sodium-cacodylate, pH6.5, 200mM magnesium-chloride, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.954 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 22, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 7102 / Num. obs: 7102 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.2 / % possible all: 99.3

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XTV

1xtv


Resolution: 2.8→25 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 334 -RANDOM
Rwork0.226 ---
all-7102 --
obs-7102 99.9 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å27.21 Å20 Å2
2--0.3 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 55 10 1760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3

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