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- PDB-1jlr: STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE GTP COMPLEX 2 M... -

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Basic information

Entry
Database: PDB / ID: 1jlr
TitleSTRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE GTP COMPLEX 2 MUTANT C128V
ComponentsUracil Phosphoribosyltransferase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / UPRTASE / GTP activated / tetramer
Function / homology
Function and homology information


uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / GTP binding
Similarity search - Function
Uracil phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
Model detailsURACIL PHOSPHORIBOSYLTRANSFERASE (E.C.2.4.2.9)
AuthorsSchumacher, M.A. / Bashor, C.J. / Otsu, K. / Zu, S. / Parry, R. / Ulmman, B. / Brennan, R.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase.
Authors: Schumacher, M.A. / Bashor, C.J. / Song, M.H. / Otsu, K. / Zhu, S. / Parry, R.J. / Ullman, B. / Brennan, R.G.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil Phosphoribosyltransferase
B: Uracil Phosphoribosyltransferase
D: Uracil Phosphoribosyltransferase
C: Uracil Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,08516
Polymers110,2334
Non-polymers2,85212
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20210 Å2
ΔGint-109 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.600, 141.800, 71.400
Angle α, β, γ (deg.)90.00, 115.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uracil Phosphoribosyltransferase


Mass: 27558.246 Da / Num. of mol.: 4 / Mutation: C1128V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pBACE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q26998, uracil phosphoribosyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Citrate buffer, NaCl, Ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
pH: 4.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M1reservoirNaCl
215 mMsodium citrate/phosphate1reservoirpH4.7
310 %PEG34001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 23, 1994 / Details: yale mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→16.1 Å / Num. obs: 34646 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 10.6
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2240 / Rsym value: 0.143 / % possible all: 67
Reflection
*PLUS
Num. measured all: 77473
Reflection shell
*PLUS
Highest resolution: 2.4 Å

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Processing

Software
NameClassification
CNSrefinement
bioteXdata reduction
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BD3

1bd3


Resolution: 2.45→16.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 522583.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3437 9.9 %RANDOM
Rwork0.184 ---
obs-34646 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.5739 Å2 / ksol: 0.300439 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å21.81 Å2
2---1.64 Å20 Å2
3----1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.45→16.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7496 0 168 159 7823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 433 9.9 %
Rwork0.276 3956 -
obs-4500 66.1 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.276

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