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- PDB-1xtu: Sulfolobus solfataricus uracil phosphoribosyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 1xtu
TitleSulfolobus solfataricus uracil phosphoribosyltransferase in complex with uridine 5'-monophosphate (UMP) and cytidine 5'-triphosphate (CTP)
ComponentsProbable uracil phosphoribosyltransferase
KeywordsTRANSFERASE / Tetramer / type 1 phosphoribosyltransferase / UMP and CTP complex
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / hypoxanthine phosphoribosyltransferase activity / UMP salvage / IMP salvage / GTP binding ...uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / hypoxanthine phosphoribosyltransferase activity / UMP 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
CYTIDINE-5'-TRIPHOSPHATE / URIDINE-5'-MONOPHOSPHATE / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArent, S. / Harris, P. / Jensen, K.F. / Larsen, S.
CitationJournal: 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
DepositionOct 24, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 8, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Probable uracil phosphoribosyltransferase
B: Probable uracil phosphoribosyltransferase
C: Probable uracil phosphoribosyltransferase
D: Probable uracil phosphoribosyltransferase
E: Probable uracil phosphoribosyltransferase
F: Probable uracil phosphoribosyltransferase
G: Probable uracil phosphoribosyltransferase
H: Probable uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,89324
Polymers193,4358
Non-polymers6,45916
Water0
1
A: Probable uracil phosphoribosyltransferase
D: Probable uracil phosphoribosyltransferase
E: Probable uracil phosphoribosyltransferase
H: Probable uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,94712
Polymers96,7174
Non-polymers3,2298
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17650 Å2
ΔGint-76 kcal/mol
Surface area29550 Å2
MethodPISA
2
B: Probable uracil phosphoribosyltransferase
C: Probable uracil phosphoribosyltransferase
F: Probable uracil phosphoribosyltransferase
G: Probable uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,94712
Polymers96,7174
Non-polymers3,2298
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17690 Å2
ΔGint-79 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.670, 76.510, 91.450
Angle α, β, γ (deg.)109.00, 90.76, 115.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 24179.348 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: upp / Plasmid: pUHE23-2 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830
References: UniProt: Q980Q4, uracil phosphoribosyltransferase
#2: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H16N3O14P3

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.098 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2002 / Details: Bent mirror
RadiationMonochromator: Si(III) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.098 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 40931 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 56.8 Å2 / Rsym value: 0.116 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.91 Å / Mean I/σ(I) obs: 1.9 / Num. unique all: 3994 / Rsym value: 0.45 / % possible all: 97.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Sulfolobus solfataricus UPRTase PDB ID 1XTT

1xtt


Resolution: 2.8→24.75 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1961 -random
Rwork0.222 ---
obs-39575 98.5 %-
Displacement parametersBiso mean: 41.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13560 0 400 0 13960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.8→2.91 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.35 179 -
Rwork0.357 --
obs-3764 97.8 %

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