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- PDB-5k51: Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase ... -

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Basic information

Entry
Database: PDB / ID: 5k51
TitleTrypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with a 9-[5-(phosphonoheptyl]hypoxanthine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / inhibitor / complex / dimer / enzyme
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / nuclear lumen / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / nuclear lumen / 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-6QD / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.956 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 22, 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 phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0328
Polymers96,8874
Non-polymers1,1454
Water86548
1
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0164
Polymers48,4442
Non-polymers5722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-15 kcal/mol
Surface area14530 Å2
MethodPISA
2
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0164
Polymers48,4442
Non-polymers5722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-13 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.093, 88.633, 94.664
Angle α, β, γ (deg.)90.00, 107.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase / / HGPRTase


Mass: 24221.775 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-6QD / 5-(6-oxidanylidene-3~{H}-purin-9-yl)pentylphosphonic acid / 9-[5-(phosphonoheptyl]hypoxanthine


Mass: 286.224 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N4O4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2 M sodium iodide, 0.1 M Bis-Tris propane
PH range: 6.5

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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: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.956→46.46 Å / Num. obs: 18891 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.142 / Rsym value: 0.114 / Net I/σ(I): 5.9
Reflection shellResolution: 2.96→3.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.6 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHASESphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq


Resolution: 2.956→46.46 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.72
RfactorNum. reflection% reflection
Rfree0.2942 1886 10 %
Rwork0.2462 --
obs0.251 18864 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.956→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 0 76 54 5366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025414
X-RAY DIFFRACTIONf_angle_d0.4687358
X-RAY DIFFRACTIONf_dihedral_angle_d13.7013238
X-RAY DIFFRACTIONf_chiral_restr0.044864
X-RAY DIFFRACTIONf_plane_restr0.003920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9563-3.03630.32251410.28621248X-RAY DIFFRACTION97
3.0363-3.12560.35971420.30731298X-RAY DIFFRACTION99
3.1256-3.22640.33221430.29811292X-RAY DIFFRACTION99
3.2264-3.34170.33681440.27411311X-RAY DIFFRACTION100
3.3417-3.47550.32031420.2691298X-RAY DIFFRACTION100
3.4755-3.63360.32881420.25671325X-RAY DIFFRACTION100
3.6336-3.82510.30161510.2541316X-RAY DIFFRACTION100
3.8251-4.06460.30371460.22431296X-RAY DIFFRACTION100
4.0646-4.37820.23251460.21761321X-RAY DIFFRACTION100
4.3782-4.81840.2481420.19281310X-RAY DIFFRACTION100
4.8184-5.51470.28271490.22841306X-RAY DIFFRACTION100
5.5147-6.94420.28371460.25011328X-RAY DIFFRACTION100
6.9442-46.46270.29221520.25441329X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -36.8062 Å / Origin y: 20.7829 Å / Origin z: 21.8583 Å
111213212223313233
T0.3545 Å2-0.0156 Å2-0.0913 Å2-0.0853 Å20.0368 Å2--0.205 Å2
L0.3647 °2-0.2844 °2-0.8252 °2-0.6619 °20.782 °2--2.8236 °2
S-0.0399 Å °-0.0571 Å °-0.058 Å °0.0267 Å °-0.0923 Å °0.006 Å °-0.0937 Å °0.0892 Å °0.1185 Å °
Refinement TLS groupSelection details: all

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