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- PDB-4i71: Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Gua... -

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Basic information

Entry
Database: PDB / ID: 4i71
TitleCrystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with a trypanocidal compound
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-AGV / 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: 1.28 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 8, 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 / 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_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_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_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)36,8448
Polymers36,1681
Non-polymers6767
Water5,080282
1
A: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)73,68816
Polymers72,3352
Non-polymers1,35314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3080 Å2
ΔGint-12 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.360, 72.350, 133.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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, 289 molecules

#2: Chemical ChemComp-AGV / (2R,3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidine-3,4-diol


Mass: 279.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N5O3
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris, 19% PEGMME2000, 10mM Ni2SO4, pH 8.0, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010
RadiationMonochromator: Silicon crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.28→133.3 Å / Num. all: 78467 / Num. obs: 78467 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 17.811 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
1.28-1.321.60.4780.2642.8455786007347234720.35357.8
1.32-1.350.3560.2284.1613938584054840.28693.9
1.35-1.390.2820.1955.3716641570156780.23999.6
1.39-1.440.2220.1586.4716169551454990.19499.7
1.44-1.480.180.1297.8215830537653620.15899.7
1.48-1.540.1320.0999.8315318520551930.12199.8
1.54-1.590.1080.08111.714720498049640.199.7
1.59-1.660.0880.06813.7814245481847900.08399.4
1.66-1.730.0740.05815.6813781465346270.07199.4
1.73-1.820.0580.05117.9313220444844160.06299.3
1.82-1.910.0480.04320.2612415420041510.05398.8
1.91-2.030.0390.03723.1311871402339710.04698.7
2.03-2.170.0330.03525.4511027374636760.04298.1
2.17-2.340.0310.03627.0310672354534600.04397.6
2.34-2.570.0350.06130.6918322326032470.06799.6
2.57-2.870.0320.05533.4118686294529370.0699.7
2.87-3.320.0280.04635.5316374262026100.05199.6
3.32-4.060.0230.04238.4413974224322290.04699.4
4.06-5.740.0230.0437.7810021173717080.04498.3
5.74-1330.0230.03834.86510210399930.04395.6

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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: 1KIC

1kic


Resolution: 1.28→133.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1482 / WRfactor Rwork: 0.1262 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9388 / SU B: 0.99 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0405 / SU Rfree: 0.0381 / Isotropic thermal model: Individual anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1467 3944 5 %RANDOM
Rwork0.1259 ---
obs0.1269 78467 95.8 %-
all-78467 --
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: 52.47 Å2 / Biso mean: 14.8256 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.28→133.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 33 282 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222646
X-RAY DIFFRACTIONr_bond_other_d0.0010.021767
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9713607
X-RAY DIFFRACTIONr_angle_other_deg1.03734351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48224.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97115450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5231510
X-RAY DIFFRACTIONr_chiral_restr0.1210.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_mcbond_it2.3082.51659
X-RAY DIFFRACTIONr_mcbond_other1.4862.5662
X-RAY DIFFRACTIONr_mcangle_it3.10632693
X-RAY DIFFRACTIONr_scbond_it4.0234987
X-RAY DIFFRACTIONr_scangle_it5.4975.5908
X-RAY DIFFRACTIONr_rigid_bond_restr1.9934413
X-RAY DIFFRACTIONr_sphericity_free11.8173287
X-RAY DIFFRACTIONr_sphericity_bonded4.94934349
LS refinement shellResolution: 1.284→1.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 161 -
Rwork0.177 3303 -
all-3464 -
obs--57.69 %

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