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- PDB-5jv5: Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase ... -

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Basic information

Entry
Database: PDB / ID: 5jv5
TitleTrypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with Guanosine 5' monophosphate
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / complex / dimer / enzyme
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / ciliary plasm / nuclear lumen ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / ciliary plasm / nuclear lumen / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytoplasm / cytosol
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
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 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 10, 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 / struct_conn
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 / _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

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,65112
Polymers48,4442
Non-polymers1,20810
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-138 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.944, 111.711, 45.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-433-

HOH

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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-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.73→48.01 Å / Num. obs: 13262 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.16 / Net I/av σ(I): 8.6 / Net I/σ(I): 8.6
Reflection shellResolution: 2.73→2.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASESphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq


Resolution: 2.73→48.011 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 1319 9.99 %
Rwork0.2362 --
obs0.2399 13206 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→48.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 72 57 2968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022963
X-RAY DIFFRACTIONf_angle_d0.5584033
X-RAY DIFFRACTIONf_dihedral_angle_d16.4181767
X-RAY DIFFRACTIONf_chiral_restr0.043470
X-RAY DIFFRACTIONf_plane_restr0.003500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7298-2.83910.38591440.33951286X-RAY DIFFRACTION99
2.8391-2.96830.31831420.29511282X-RAY DIFFRACTION100
2.9683-3.12470.38031440.28651306X-RAY DIFFRACTION100
3.1247-3.32040.29991440.27471305X-RAY DIFFRACTION100
3.3204-3.57670.31421450.26311303X-RAY DIFFRACTION100
3.5767-3.93650.24521450.21491312X-RAY DIFFRACTION100
3.9365-4.50580.20391480.19121337X-RAY DIFFRACTION100
4.5058-5.67540.23551490.18051344X-RAY DIFFRACTION100
5.6754-48.01790.24831580.22221412X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.9585 Å / Origin y: 27.784 Å / Origin z: 14.7837 Å
111213212223313233
T0.1198 Å2-0.0053 Å2-0.0068 Å2-0.3743 Å2-0.0088 Å2--0.0903 Å2
L2.0151 °20.4172 °20.0972 °2-1.156 °2-0.1667 °2--0.5112 °2
S0.1384 Å °-0.0394 Å °-0.0861 Å °0.0712 Å °-0.1062 Å °-0.051 Å °-0.0029 Å °0.0534 Å °-0.0177 Å °
Refinement TLS groupSelection details: all

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