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

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Basic information

Entry
Database: PDB / ID: 1xtt
TitleSulfolobus solfataricus uracil phosphoribosyltransferase in complex with uridine 5'-monophosphate (UMP)
ComponentsProbable uracil phosphoribosyltransferase
KeywordsTRANSFERASE / Tetramer / type 1 phosphoribosyltransferase / UMP complex
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
ACETIC ACID / URIDINE-5'-MONOPHOSPHATE / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,13410
Polymers96,7174
Non-polymers1,4176
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-90 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.840, 97.480, 73.440
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24179.348 Da / Num. of mol.: 4
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


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.18 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium acetate, pH 5.5, 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: 1.08535 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 22, 2001 / Details: Bent mirror
RadiationMonochromator: Si(III) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08535 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 72112 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.142 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 3466 / Rsym value: 0.41 / % possible all: 90.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→24.43 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1758 -random
Rwork0.193 ---
obs-72053 94.2 %-
Displacement parametersBiso mean: 19.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6674 0 84 700 7458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.8→1.83 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.274 173 -
Rwork0.247 --
obs-3277 91 %

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