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- PDB-1bd4: UPRT-URACIL COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1bd4
TitleUPRT-URACIL COMPLEX
ComponentsURACIL PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / UPRT / URACIL / GLYCOSYLTRANSFERASE / COMPLEX
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 / URACIL / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSchumacher, M.A. / Carter, D. / Scott, D. / Roos, D. / Ullman, B. / Brennan, R.G.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
Authors: Schumacher, M.A. / Carter, D. / Scott, D.M. / Roos, D.S. / Ullman, B. / Brennan, R.G.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _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
D: URACIL PHOSPHORIBOSYLTRANSFERASE
C: URACIL PHOSPHORIBOSYLTRANSFERASE
B: URACIL PHOSPHORIBOSYLTRANSFERASE
A: URACIL PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,44116
Polymers110,2334
Non-polymers1,20812
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15350 Å2
ΔGint-83 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.390, 141.770, 71.460
Angle α, β, γ (deg.)90.00, 114.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
URACIL PHOSPHORIBOSYLTRANSFERASE / / UPRTASE


Mass: 27558.246 Da / Num. of mol.: 4 / Mutation: C128V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q26998, uracil phosphoribosyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-URA / URACIL / Uracil


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


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STRUCTURE HAS TWO PHOSPHATE MOLECULES (USED IN CRYSTALLIZATION). ONE PHOSPHATE FOUND IN THE ...THE STRUCTURE HAS TWO PHOSPHATE MOLECULES (USED IN CRYSTALLIZATION). ONE PHOSPHATE FOUND IN THE ACTIVE SITE NEAR HELIX 5. THERE IS A URACIL MOLECULE BOUND IN EACH SUBUNIT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
210 mMdithiothreitol1drop
325-40 mg/mlprotein1drop
41.0 Mammonium phosphate1reservoir
50.1 Mcitrate1reservoir
60.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 298 K
DetectorDate: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. obs: 53303 / % possible obs: 87 % / Num. measured all: 111427 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 2.23 Å / Mean I/σ(I) obs: 3.9

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.2→10 Å / σ(F): 1
Details: THERE IS A TETRAMER (CHAINS A, B, C, D) IN THE ASYMMETRIC UNIT. THERE ARE FOUR IN THE ASYMMETRIC UNIT FOR SPACE GROUP P21. P21 SPACE GROUP CAN BE TRANSFORMED TO C2221. SOLVED AS P21 FOR ...Details: THERE IS A TETRAMER (CHAINS A, B, C, D) IN THE ASYMMETRIC UNIT. THERE ARE FOUR IN THE ASYMMETRIC UNIT FOR SPACE GROUP P21. P21 SPACE GROUP CAN BE TRANSFORMED TO C2221. SOLVED AS P21 FOR TECHNICAL REASONS. THE N-TERMINAL MET IS CLEAVED OFF IN ESCHERICHIA COLI. RESIDUES 2 THROUGH 20 ARE DISORDERED AND NOT INCLUDED. STRUCTURE INCLUDES RESIDUES 21 TO 244 OF EACH MONOMER. THERE IS A TETRAMER (CHAINS A, B, C, D) IN THE ASYMMETRIC UNIT. THERE ARE FOUR IN THE ASYMMETRIC UNIT FOR SPACE GROUP P21. P21 SPACE GROUP CAN BE TRANSFORMED TO C2221. SOLVED AS P21 FOR TECHNICAL REASONS.
RfactorNum. reflection% reflection
Rwork0.194 --
obs-53303 87 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 72 241 7465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.903
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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