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- PDB-4i75: Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Gua... -

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Basic information

Entry
Database: PDB / ID: 4i75
TitleCrystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with the NiTris metalorganic complex
ComponentsInosine-adenosine-guanosine-nucleoside hydrolase
KeywordsHYDROLASE / nucleoside hydrolase / open (alpha / beta) structure / NH fold
Function / homology
Function and homology information


purine nucleosidase / purine nucleosidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / glycosome / purine ribonucleoside salvage / purine nucleoside catabolic process / 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
NICKEL (II) ION / Inosine-adenosine-guanosine-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 1.2Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)73,55418
Polymers72,3352
Non-polymers1,21916
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-86 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.700, 134.890, 60.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 3 / Auth seq-ID: 2 - 326 / Label seq-ID: 5 - 329

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 36167.582 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.6
Details: 0.1M Tris, 23% PEGMME2000, 10mM Ni2SO4, pH 8.6, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→68 Å / Num. all: 54442 / Num. obs: 54442 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 25.787 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.29
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
1.8-1.853.50.790.5612.6134243990378037800.6694.7
1.85-1.90.8720.4223.514588390539010.49499.9
1.9-1.950.8940.3424.2114151379037850.499.9
1.95-2.010.9330.2685.3313706366536600.31399.9
2.01-2.080.9540.2176.4213388359435840.25499.7
2.08-2.150.9660.1787.7612827343134260.20899.9
2.15-2.230.980.1469.2112556335533500.17199.9
2.23-2.330.9860.11810.8812044322932240.13899.8
2.33-2.430.9870.10212.611596310230960.1299.8
2.43-2.550.9910.08913.9211069296529620.10499.9
2.55-2.680.9940.07316.6310533282128190.08599.9
2.68-2.850.9960.06118.769968269126860.07199.8
2.85-3.040.9960.05221.699378252325200.06199.9
3.04-3.290.9970.04324.728634235023450.0599.8
3.29-3.60.9980.03529.517932219221830.04199.6
3.6-4.030.9990.02933.517117197919690.03499.5
4.03-4.650.9990.02735.996324177617710.03299.7
4.65-5.70.9990.02634.95209151015040.0399.6
5.7-8.050.9990.02534.784099118811850.02999.7
8.050.9990.02237.1322007186920.02796.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TbbIAGNH-363 complex

Resolution: 1.8→48.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2119 / WRfactor Rwork: 0.1696 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8527 / SU B: 6.717 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1442 / SU Rfree: 0.1345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 2761 5.1 %RANDOM
Rwork0.1804 ---
obs0.1825 54442 99.4 %-
all-54442 --
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: 66.02 Å2 / Biso mean: 20.222 Å2 / Biso min: 4.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---0.96 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 51 492 5515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225173
X-RAY DIFFRACTIONr_bond_other_d0.0040.023431
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9637040
X-RAY DIFFRACTIONr_angle_other_deg1.16438451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2435661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02525.144208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0415878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1411518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02966
X-RAY DIFFRACTIONr_mcbond_it0.8071.53275
X-RAY DIFFRACTIONr_mcbond_other0.2721.51306
X-RAY DIFFRACTIONr_mcangle_it1.43725309
X-RAY DIFFRACTIONr_scbond_it2.57731898
X-RAY DIFFRACTIONr_scangle_it3.9794.51722
X-RAY DIFFRACTIONr_sphericity_free14.508311
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1874TIGHT POSITIONAL0.050.05
2194LOOSE POSITIONAL0.095
1874TIGHT THERMAL0.240.5
2194LOOSE THERMAL0.2210
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 194 -
Rwork0.271 3575 -
all-3769 -
obs--94.65 %
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)
11.1733-0.37510.01541.413-0.34241.13140.00680.0286-0.0578-0.043-0.0205-0.00860.10750.04940.01370.01110.00360.00420.0046-0.00510.018212.46918.558-3.67
21.15470.52080.00311.2962-0.06950.8211-0.02590.02140.1105-0.05990.04160.0653-0.10680.0358-0.01580.0272-0.002-0.01660.02660.00270.040111.91750.107-26.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 327
2X-RAY DIFFRACTION2B2 - 327

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