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- PDB-1p19: Hypoxanthine Phosphoribosyltransferase from Trypanosoma cruzi, in... -

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Basic information

Entry
Database: PDB / ID: 1p19
TitleHypoxanthine Phosphoribosyltransferase from Trypanosoma cruzi, in complex with the product IMP
Componentshypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / PRODUCT COMPLEX
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMedrano, F.J. / Eakin, A.E. / Craig III, S.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Interactions at the dimer interface influence the relative efficiencies for purine nucleotide synthesis and pyrophosphorolysis in a phosphoribosyltransferase.
Authors: Canyuk, B. / Medrano, F.J. / Wenck, M.A. / Focia, P.J. / Eakin, A.E. / Craig III, S.P.
History
DepositionApr 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: hypoxanthine phosphoribosyltransferase
B: hypoxanthine phosphoribosyltransferase
C: hypoxanthine phosphoribosyltransferase
D: hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7748
Polymers102,3824
Non-polymers1,3934
Water14,052780
1
A: hypoxanthine phosphoribosyltransferase
B: hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,1912
Non-polymers6962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-20 kcal/mol
Surface area16920 Å2
MethodPISA
2
C: hypoxanthine phosphoribosyltransferase
D: hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,1912
Non-polymers6962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-17 kcal/mol
Surface area16930 Å2
MethodPISA
3
A: hypoxanthine phosphoribosyltransferase
B: hypoxanthine phosphoribosyltransferase
hetero molecules

C: hypoxanthine phosphoribosyltransferase
D: hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7748
Polymers102,3824
Non-polymers1,3934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area12090 Å2
ΔGint-42 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.940, 121.020, 52.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThere are two copies of the biological dimer in the asymmetric unit

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Components

#1: Protein
hypoxanthine phosphoribosyltransferase


Mass: 25595.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: HGPRT / Plasmid: pTcPRT / Production host: Escherichia coli (E. coli)
References: UniProt: Q27796, UniProt: Q4DRC4*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG 6000, Sodium Acetate, Ammonium Acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 1999
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 44180 / Num. obs: 44180 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.9 / % possible all: 87.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.261 -random
Rwork0.193 --
all0.193 44180 -
obs0.193 44180 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 92 780 6944

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