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- PDB-5jsq: Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase ... -

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Basic information

Entry
Database: PDB / ID: 5jsq
TitleTrypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with a 9-[7-(phosphonoheptyl]guanine
Componentshypoxanthine-guanine phosphoribosyltranferase
KeywordsTRANSFERASE / inhibitor / complex / dimer / enzyme
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / nuclear lumen / glycosome / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / nuclear lumen / glycosome / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6MS / DI(HYDROXYETHYL)ETHER / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsTeran, D. / Guddat, L.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structures and inhibition of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltransferase.
Authors: Teran, D. / Hockova, D. / Cesnek, M. / Zikova, A. / Naesens, L. / Keough, D.T. / Guddat, L.W.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypoxanthine-guanine phosphoribosyltranferase
B: hypoxanthine-guanine phosphoribosyltranferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,80313
Polymers48,4442
Non-polymers1,36011
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-60 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.376, 108.787, 44.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-565-

HOH

31B-437-

HOH

41B-548-

HOH

51B-556-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypoxanthine-guanine phosphoribosyltranferase / HGPRTase


Mass: 24221.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli)
References: UniProt: Q07010, hypoxanthine phosphoribosyltransferase

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Non-polymers , 6 types, 412 molecules

#2: Chemical ChemComp-6MS / [6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)hexyl]phosphonic acid / 9-[7-(phosphonoheptyl]guanine


Mass: 315.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O4P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris
PH range: 5-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.5→43.291 Å / Num. obs: 73902 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.112 / Net I/av σ(I): 11.1 / Net I/σ(I): 11.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2 / Rsym value: 0.411 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHASESphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TC2

1tc2


Resolution: 1.503→43.291 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.25
RfactorNum. reflection% reflection
Rfree0.1781 2000 2.71 %
Rwork0.161 --
obs0.1615 73865 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.503→43.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 86 405 3214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163025
X-RAY DIFFRACTIONf_angle_d1.54136
X-RAY DIFFRACTIONf_dihedral_angle_d18.4311845
X-RAY DIFFRACTIONf_chiral_restr0.099480
X-RAY DIFFRACTIONf_plane_restr0.009506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5032-1.54080.27611380.25634961X-RAY DIFFRACTION97
1.5408-1.58250.22541410.19885052X-RAY DIFFRACTION100
1.5825-1.6290.17591410.1835089X-RAY DIFFRACTION100
1.629-1.68160.18521410.17585068X-RAY DIFFRACTION100
1.6816-1.74170.21361420.1695078X-RAY DIFFRACTION100
1.7417-1.81150.18691420.16755091X-RAY DIFFRACTION100
1.8115-1.89390.19541410.15835102X-RAY DIFFRACTION100
1.8939-1.99380.18381420.15395104X-RAY DIFFRACTION100
1.9938-2.11870.15261430.14635147X-RAY DIFFRACTION100
2.1187-2.28230.18761440.14595121X-RAY DIFFRACTION100
2.2823-2.51190.15431430.14925164X-RAY DIFFRACTION100
2.5119-2.87530.18631440.15695192X-RAY DIFFRACTION100
2.8753-3.62230.17331450.15175240X-RAY DIFFRACTION100
3.6223-43.30870.1591530.1635456X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.1838 Å / Origin y: 27.168 Å / Origin z: 47.7179 Å
111213212223313233
T0.0734 Å20.0101 Å2-0.0016 Å2-0.0818 Å20.0037 Å2--0.0204 Å2
L1.8068 °20.4161 °2-0.0352 °2-0.9277 °20.0325 °2--0.5379 °2
S0.025 Å °0.1217 Å °-0.0068 Å °-0.0657 Å °-0.0066 Å °-0.0041 Å °-0.0139 Å °-0.0107 Å °-0.0196 Å °
Refinement TLS groupSelection details: all

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