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- PDB-1jls: STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE URACIL/CPR 2 MU... -

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Basic information

Entry
Database: PDB / ID: 1jls
TitleSTRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE URACIL/CPR 2 MUTANT C128V
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / UPRTASE / ternary complex / UPRT-cprpp-uracil
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
PHOSPHATE ION / Chem-PRP / URACIL / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchumacher, M.A. / Bashor, C.J. / Otsu, K. / Zu, S. / Parry, R. / Ullman, 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 16, 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,95019
Polymers110,2334
Non-polymers1,71715
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-119 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.400, 111.400, 71.900
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules BADC

#1: Protein
Uracil phosphoribosyltransferase


Mass: 27558.246 Da / Num. of mol.: 4 / Mutation: C128V
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
#5: 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

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Non-polymers , 4 types, 132 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: NaCl, citrate/phosphate buffer, PEG 3400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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: Apr 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: 2.5→60 Å / Num. obs: 32692 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4008 / Rsym value: 0.265 / % possible all: 56
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 60 Å / Num. measured all: 99823
Reflection shell
*PLUS
Highest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
MERLOTphasing
CNS1refinement
bioteXdata reduction
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BD3

1bd3


Resolution: 2.5→60.03 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1115798.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 3240 9.9 %RANDOM
Rwork0.232 ---
obs-32692 84.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 89.708 Å2 / ksol: 0.342656 e/Å3
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å22.09 Å2
2---12.97 Å20 Å2
3---12.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.5→60.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7068 0 100 118 7286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 413 9.9 %
Rwork0.372 3760 -
obs--64.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2.18
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.409 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.372

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