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- PDB-4i70: Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Gua... -

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Basic information

Entry
Database: PDB / ID: 4i70
TitleCrystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase
ComponentsInosine-adenosine-guanosine-nucleoside hydrolase
KeywordsHYDROLASE / nucleoside hydrolase / Open (alpha / beta) structure / NH fold / Nucleotide metabolism
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
Inosine-adenosine-guanosine-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 1.2Apr 3, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)35,9252
Polymers35,8851
Non-polymers401
Water5,783321
1
A: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)71,8514
Polymers71,7712
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area2100 Å2
ΔGint-31 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.040, 48.040, 216.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

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Components

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


Mass: 35885.305 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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 38.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.8
Details: 0.2M ammonium acetate, 18% PEG3350, pH 4.8, 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(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→72.037 Å / Num. all: 38235 / Num. obs: 38235 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 25.479 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 22.52
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
1.6-1.77.50.2590.3895.94467806256621562150.41899.3
1.7-1.80.1670.2618.7237327497749550.2899.6
1.8-20.0950.15313.854590727172490.16499.7
2-2.50.0470.15424.7283679954895410.16299.9
2.5-30.0310.18334.9864344427942790.189100
3-40.0210.08145.4850359342134200.084100
4-60.0160.05353.9225966178817880.055100
6-100.0150.04754.2684256076070.049100
10-500.0120.03658.221711841810.03898.4

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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: IAGNH-363

Resolution: 1.6→72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1786 / WRfactor Rwork: 0.1394 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9075 / SU B: 2.846 / SU ML: 0.046 / SU R Cruickshank DPI: 0.1162 / SU Rfree: 0.0822 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 1916 5 %RANDOM
Rwork0.1419 ---
obs0.1438 38232 99.75 %-
all-38232 --
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: 55.34 Å2 / Biso mean: 19.1117 Å2 / Biso min: 8.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 1 321 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222546
X-RAY DIFFRACTIONr_bond_other_d0.0010.021707
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9613474
X-RAY DIFFRACTIONr_angle_other_deg0.9963.0014209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13725102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08215444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3191510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_mcbond_it1.3051.51609
X-RAY DIFFRACTIONr_mcbond_other0.5421.5645
X-RAY DIFFRACTIONr_mcangle_it2.05222616
X-RAY DIFFRACTIONr_scbond_it3.033937
X-RAY DIFFRACTIONr_scangle_it4.6194.5847
X-RAY DIFFRACTIONr_rigid_bond_restr1.42934253
X-RAY DIFFRACTIONr_sphericity_free7.2933322
X-RAY DIFFRACTIONr_sphericity_bonded2.94734188
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 131 -
Rwork0.146 2600 -
all-2731 -
obs--99.35 %

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