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

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Basic information

Entry
Database: PDB / ID: 6apu
TitleCrystal structure of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Purine salvage / acyclic nucleoside phosphonate
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 / 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-3L6 / DI(HYDROXYETHYL)ETHER / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.842 Å
AuthorsTeran, D. / Guddat, L.
CitationJournal: PLoS Negl Trop Dis / Year: 2018
Title: Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery.
Authors: Dolezelova, E. / Teran, D. / Gahura, O. / Kotrbova, Z. / Prochazkova, M. / Keough, D. / Spacek, P. / Hockova, D. / Guddat, L. / Zikova, A.
History
DepositionAug 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)49,71214
Polymers48,4442
Non-polymers1,26912
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-97 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.883, 108.890, 44.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 440 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-3L6 / (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid


Mass: 359.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22N7O4P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 48.7 %
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: 5-7

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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: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.84→47.44 Å / Num. obs: 41021 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rpim(I) all: 0.066 / Net I/σ(I): 12.4
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2386 / Rpim(I) all: 0.371 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq


Resolution: 1.842→43.493 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 1997 4.88 %
Rwork0.1502 --
obs0.1522 40951 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.842→43.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 76 434 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023080
X-RAY DIFFRACTIONf_angle_d1.5964206
X-RAY DIFFRACTIONf_dihedral_angle_d12.5452498
X-RAY DIFFRACTIONf_chiral_restr0.116484
X-RAY DIFFRACTIONf_plane_restr0.011525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.842-1.88810.25781320.24032580X-RAY DIFFRACTION95
1.8881-1.93910.24681420.18052778X-RAY DIFFRACTION100
1.9391-1.99620.19511400.16342721X-RAY DIFFRACTION100
1.9962-2.06060.21661420.15162774X-RAY DIFFRACTION100
2.0606-2.13430.19271420.14482765X-RAY DIFFRACTION100
2.1343-2.21970.19741410.1422756X-RAY DIFFRACTION100
2.2197-2.32070.18491420.13712771X-RAY DIFFRACTION100
2.3207-2.44310.19221420.1372782X-RAY DIFFRACTION100
2.4431-2.59610.17811430.1382777X-RAY DIFFRACTION100
2.5961-2.79650.18221430.14412803X-RAY DIFFRACTION100
2.7965-3.07790.17811440.14752795X-RAY DIFFRACTION100
3.0779-3.52310.18951460.14222843X-RAY DIFFRACTION100
3.5231-4.43810.15291450.13332843X-RAY DIFFRACTION100
4.4381-43.5050.21571530.17192966X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4277-0.38190.88842.0638-0.78231.4940.08160.13030.0617-0.0349-0.1044-0.01550.02320.10790.00770.0926-0.00890.02340.0836-0.00580.078429.0613143.177751.1685
23.0609-1.20660.36074.1782-0.0931.81140.40381.1095-0.0071-0.527-0.30780.4237-0.03660.1603-0.09480.18840.0531-0.00960.32090.08230.084532.9429145.547839.8282
33.67710.01030.36190.8940.25642.15110.14790.6179-0.3106-0.0734-0.0829-0.19050.06180.2862-0.02010.08260.05020.01810.2216-0.05190.106138.5648134.856145.4531
43.5869-2.42781.72986.2465-1.9564.3396-0.0542-0.21150.92430.48770.08750.0405-0.4075-0.11010.0210.18950.01670.07170.1674-0.07550.33998.4436148.130658.6861
52.53690.4593-0.38282.72211.11142.33530.06090.0268-0.31810.1501-0.0346-0.06430.1662-0.0265-0.01380.1069-0.0067-0.02720.08260.01420.137918.5479124.849853.0417
63.03630.19510.3885.88071.4422.9424-0.09140.4994-0.451-0.6224-0.1244-0.46660.03840.2013-0.03680.14680.01310.02860.1363-0.06640.244822.565122.584743.2445
74.3513-2.8571-0.17875.31210.62792.56510.10420.4701-0.2395-0.2361-0.16960.1050.0923-0.16970.08870.1148-0.0205-0.01120.1415-0.03960.128110.0317125.498241.4161
82.21280.73890.3232.05430.11761.10260.00580.13820.1951-0.06970.01280.1772-0.0052-0.1036-0.01130.09240.02180.00190.10070.01570.11517.9199139.040148.6775
90.20950.26971.08625.3497-1.86877.41320.39761.07371.2014-0.4016-0.20080.7921-1.3019-1.5698-0.4580.44480.20140.00670.48930.2910.67026.9834158.194540.7843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 199 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 16 )
5X-RAY DIFFRACTION5chain 'B' and (resid 17 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 107 )
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 148 )
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 188 )
9X-RAY DIFFRACTION9chain 'B' and (resid 189 through 202 )

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