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

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Basic information

Entry
Database: PDB / ID: 5kap
TitleTrypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with a 9-(4-(phosphonobutil)hypoxanthine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / complex / dimer / enzyme / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-6RH / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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
DepositionJun 1, 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_seq_id / _struct_conn.ptnr2_label_asym_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)49,42213
Polymers48,4442
Non-polymers97811
Water21612
1
A: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,51814
Polymers48,4442
Non-polymers1,07412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area4430 Å2
ΔGint-138 kcal/mol
Surface area13910 Å2
MethodPISA
2
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules

B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,32612
Polymers48,4442
Non-polymers88210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4220 Å2
ΔGint-114 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.106, 93.893, 109.784
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-306-

MG

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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-6RH / 4-(6-oxidanylidene-1~{H}-purin-9-yl)butylphosphonic acid / 9-(4-(phosphonobutil)hypoxanthine


Mass: 272.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N4O4P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
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: 2.81→47.39 Å / Num. obs: 11686 / % possible obs: 98.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13
Reflection shellResolution: 2.81→2.97 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4

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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: 2.95→45.106 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3093 1018 10.01 %
Rwork0.2747 --
obs0.2782 10172 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→45.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 57 12 2658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022712
X-RAY DIFFRACTIONf_angle_d0.4993691
X-RAY DIFFRACTIONf_dihedral_angle_d15.6931620
X-RAY DIFFRACTIONf_chiral_restr0.043431
X-RAY DIFFRACTIONf_plane_restr0.004458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.10550.40291390.34051268X-RAY DIFFRACTION98
3.1055-3.30.3561430.30361280X-RAY DIFFRACTION98
3.3-3.55470.31331430.30291276X-RAY DIFFRACTION98
3.5547-3.91230.30831430.28021286X-RAY DIFFRACTION98
3.9123-4.4780.26791460.24941318X-RAY DIFFRACTION99
4.478-5.64010.32941490.24631333X-RAY DIFFRACTION99
5.6401-45.11130.28381550.27341393X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -36.4196 Å / Origin y: 32.7608 Å / Origin z: 23.6149 Å
111213212223313233
T0.7399 Å2-0.2122 Å2-0.1223 Å2-0.2825 Å20.1954 Å2--0.6532 Å2
L0.1756 °21.3258 °2-1.6643 °2-4.4556 °2-3.9023 °2--2.6895 °2
S-0.1277 Å °0.1228 Å °0.5494 Å °-0.5516 Å °0.7037 Å °0.4582 Å °0.0862 Å °-0.4533 Å °-0.1947 Å °
Refinement TLS groupSelection details: all

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