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- PDB-4i74: Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Gua... -

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Basic information

Entry
Database: PDB / ID: 4i74
TitleCrystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with compound UAMC-00312 and allosterically inhibited by a Ni2+ ion
ComponentsInosine-adenosine-guanosine-nucleoside hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / nucleoside hydrolase / open (alpha / beta) structure / NH fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


purine nucleosidase / purine nucleosidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / glycosome / purine nucleoside catabolic process / purine ribonucleoside salvage / metal ion binding / cytosol
Similarity search - Function
Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-MBY / NICKEL (II) ION / Inosine-adenosine-guanosine-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGiannese, F. / Degano, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor
Authors: Giannese, F. / Berg, M. / Van der Veken, P. / Castagna, V. / Tornaghi, P. / Augustyns, K. / Degano, M.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Transition-state complex of the purine-specific nucleoside hydrolase of T. vivax: enzyme conformational changes and implications for catalysis
Authors: Versees, W. / Barlow, J. / Steyaert, J.
#2: Journal: Biochemistry / Year: 2010
Title: Structure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei
Authors: Vandemeulebroucke, A. / Minici, C. / Bruno, I. / Muzzolini, L. / Tornaghi, P. / Parkin, D.W. / Versees, W. / Steyaert, J. / Degano, M.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism
Authors: Parkin, D.W.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_comp_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.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,03811
Polymers36,1681
Non-polymers87010
Water5,062281
1
A: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules

A: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,07622
Polymers72,3352
Non-polymers1,74120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3820 Å2
ΔGint-98 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.120, 69.420, 130.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inosine-adenosine-guanosine-nucleoside hydrolase


Mass: 36167.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.3.2960 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57ZL6, purine nucleosidase

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Non-polymers , 5 types, 291 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MBY / (2R,3R,4S)-2-(hydroxymethyl)-1-[(4-hydroxythieno[3,2-d]pyrimidin-7-yl)methyl]pyrrolidine-3,4-diol


Mass: 297.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3O4S
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsMBY 408 AND NI 406, TRS 409 PLACE THE ALTERNATE POSITIONS.

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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: 1.88 Å3/Da / Density % sol: 34.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1M Tris, 23% PEGMME2000, 10mM Ni2SO4, pH 7.6, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2010
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.68→42.91 Å / Num. all: 31441 / Num. obs: 31441 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 21.247 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
1.68-1.726.50.520.6572.94148732302228322830.71199.2
1.72-1.770.4060.5233.6214884226522630.56799.9
1.77-1.820.3590.4514.3614777217821750.48899.9
1.82-1.880.2770.3615.5214372207820780.39100
1.88-1.940.2050.2797.214615208620830.30199.9
1.94-2.010.1530.2179.5814072198619830.23499.8
2.01-2.080.1120.16912.2313861192219220.182100
2.08-2.170.0970.1414.4713477185418520.1599.9
2.17-2.270.0820.11816.8112838175417540.127100
2.27-2.380.0680.119.7112439170817080.107100
2.38-2.50.0610.0921.3111852163216320.097100
2.5-2.660.050.07325.4211173154115400.07999.9
2.66-2.840.0410.06328.3710516145414530.06899.9
2.84-3.070.0310.05133.419780136313630.055100
3.07-3.360.0240.04239.998966124112410.046100
3.36-3.760.020.03446.328086113811380.037100
3.76-4.340.0170.0349.167169102310230.032100
4.34-5.310.0160.02851.6959698608600.03100
5.31-7.510.0160.03148.5946976866860.034100
7.510.0140.02552.4324274064040.02799.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→42.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1732 / WRfactor Rwork: 0.1403 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9029 / SU B: 1.905 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1017 / SU Rfree: 0.0998 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1590 5.1 %RANDOM
Rwork0.1501 ---
obs0.1521 31439 99.89 %-
all-31439 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.15 Å2 / Biso mean: 20.6601 Å2 / Biso min: 2.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.68→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 36 281 2823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222655
X-RAY DIFFRACTIONr_bond_other_d0.0010.021754
X-RAY DIFFRACTIONr_angle_refined_deg1.681.973625
X-RAY DIFFRACTIONr_angle_other_deg1.00234331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69425.189106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35215449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.25159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_mcbond_it0.8871.51670
X-RAY DIFFRACTIONr_mcbond_other0.2581.5669
X-RAY DIFFRACTIONr_mcangle_it1.56122712
X-RAY DIFFRACTIONr_scbond_it2.4753985
X-RAY DIFFRACTIONr_scangle_it4.1244.5905
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 115 -
Rwork0.191 2166 -
all-2281 -
obs--99.17 %

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