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- PDB-6mxg: Crystal structure of Trypanosoma brucei hypoxanthine-guanine phos... -

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Basic information

Entry
Database: PDB / ID: 6mxg
TitleCrystal structure of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with XMP
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / 6-oxopurine PRTs / Purine salvage
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
XANTHOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 Å
AuthorsTeran, D. / Guddat, L.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structures of Trypanosoma brucei hypoxanthine - guanine - xanthine phosphoribosyltransferase in complex with IMP, GMP and XMP.
Authors: Teran, D. / Dolezelova, E. / Keough, D.T. / Hockova, D. / Zikova, A. / Guddat, L.W.
History
DepositionOct 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,46310
Polymers48,4442
Non-polymers1,0208
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-91 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.570, 94.370, 45.000
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypoxanthine-guanine phosphoribosyltransferase / 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
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
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: 5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.39→71.35 Å / Num. obs: 17999 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2577 / Rpim(I) all: 0.397 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq


Resolution: 2.392→47.185 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.14
RfactorNum. reflection% reflection
Rfree0.285 1787 9.99 %
Rwork0.2571 --
obs0.2613 16212 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.392→47.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 62 59 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042814
X-RAY DIFFRACTIONf_angle_d0.6213846
X-RAY DIFFRACTIONf_dihedral_angle_d13.3941011
X-RAY DIFFRACTIONf_chiral_restr0.024456
X-RAY DIFFRACTIONf_plane_restr0.003482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.392-2.45820.32861340.31331185X-RAY DIFFRACTION86
2.4582-2.53050.3151470.3041248X-RAY DIFFRACTION89
2.5305-2.61210.3591340.33211246X-RAY DIFFRACTION90
2.6121-2.70550.29851310.30431231X-RAY DIFFRACTION90
2.7055-2.81380.33771390.31811263X-RAY DIFFRACTION90
2.8138-2.94180.30081340.28171226X-RAY DIFFRACTION90
2.9418-3.09690.33031360.2941243X-RAY DIFFRACTION90
3.0969-3.29080.34011430.25931252X-RAY DIFFRACTION90
3.2908-3.54470.24311350.26191236X-RAY DIFFRACTION90
3.5447-3.90120.28131310.2411252X-RAY DIFFRACTION91
3.9012-4.46510.27271400.21521277X-RAY DIFFRACTION90
4.4651-5.62320.19261380.21741238X-RAY DIFFRACTION90
5.6232-40.62280.2881450.25271284X-RAY DIFFRACTION90

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