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- PDB-4i72: Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Gua... -

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Basic information

Entry
Database: PDB / ID: 4i72
TitleCrystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with Immucillin A
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
NICKEL (II) ION / Chem-UA2 / Inosine-adenosine-guanosine-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_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

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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)73,72316
Polymers72,3352
Non-polymers1,38814
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-81 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.750, 130.980, 63.690
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 4 / Auth seq-ID: -2 - 327 / Label seq-ID: 1 - 330

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

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 459 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UA2 / 3,4-PYRROLIDINEDIOL,2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)-2S,3S,4R,5R


Mass: 265.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.2
Details: 0.1M Tris, 22% PEGMME2000, 10mM NiSO4, pH 7.2, 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: 2.05→47.92 Å / Num. all: 38963 / Num. obs: 38963 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.344 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.39
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
2.05-2.17.40.5550.693.03208872829283128310.743100
2.1-2.160.4640.5633.720350276427640.606100
2.16-2.220.3860.4834.2719911270026990.519100
2.22-2.290.3060.395.2819465263726370.42100
2.29-2.370.2770.3356.1218670253525350.36100
2.37-2.450.2350.297.1118157246124600.312100
2.45-2.540.1910.2458.3717534238023790.264100
2.54-2.650.1440.18210.9916699226522650.196100
2.65-2.760.1280.15812.5316341221922190.17100
2.76-2.90.1020.1315.1615499211221120.14100
2.9-3.060.0790.10318.8214643200020000.111100
3.06-3.240.0590.07823.8713991190819080.084100
3.24-3.470.0420.05731.2813173181018100.061100
3.47-3.740.0310.04338.2412246168216820.046100
3.74-4.10.0260.03744.3811112153715370.04100
4.1-4.580.020.0351.4110253142914290.032100
4.58-5.290.0210.0351.298946125712570.032100
5.29-6.480.0230.03346.367543107810780.036100
6.48-9.170.0180.02652.158168588570.02899.9
9.170.0160.02259.0930135115040.02498.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2074 / WRfactor Rwork: 0.1548 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8459 / SU B: 4.846 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2279 / SU Rfree: 0.1898 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1986 5.1 %RANDOM
Rwork0.1772 ---
obs0.1801 38960 99.98 %-
all-38960 --
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: 86.48 Å2 / Biso mean: 32.0337 Å2 / Biso min: 17.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2---1.02 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 71 445 5546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225240
X-RAY DIFFRACTIONr_bond_other_d0.0010.023472
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9697131
X-RAY DIFFRACTIONr_angle_other_deg0.93338534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77125.048208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09515875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0151518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
X-RAY DIFFRACTIONr_mcbond_it0.7371.53300
X-RAY DIFFRACTIONr_mcbond_other0.2091.51324
X-RAY DIFFRACTIONr_mcangle_it1.30425342
X-RAY DIFFRACTIONr_scbond_it2.03931940
X-RAY DIFFRACTIONr_scangle_it3.1634.51787
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4157 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.250.5
MEDIUM THERMAL0.792
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 144 -
Rwork0.227 2683 -
all-2827 -
obs--100 %

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