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- PDB-1kie: Inosine-adenosine-guanosine preferring nucleoside hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 1kie
TitleInosine-adenosine-guanosine preferring nucleoside hydrolase from Trypanosoma vivax: Asp10Ala mutant in complex with 3-deaza-adenosine
Componentsinosine-adenosine-guanosine preferring nucleoside hydrolase
KeywordsHYDROLASE / Rossmann-fold-like motif
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / nucleobase-containing compound metabolic process / metal ion binding
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
3-DEAZA-ADENOSINE / NICKEL (II) ION / IAG-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma vivax (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS TO INOSINE COMPLEX, PDB ENTRY 1KIC / Resolution: 2 Å
AuthorsVersees, W. / Decanniere, K. / Van Holsbeke, E. / Devroede, N. / Steyaert, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax.
Authors: Versees, W. / Decanniere, K. / Van Holsbeke, E. / Devroede, N. / Steyaert, J.
History
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_conn.ptnr2_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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: inosine-adenosine-guanosine preferring nucleoside hydrolase
B: inosine-adenosine-guanosine preferring nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0217
Polymers75,3502
Non-polymers6715
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-44 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.27, 72.96, 71.53
Angle α, β, γ (deg.)90, 98.18, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein inosine-adenosine-guanosine preferring nucleoside hydrolase / IAG-NUCLEOSIDE HYDROLASE / IAG-NH


Mass: 37674.973 Da / Num. of mol.: 2 / Mutation: D10A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma vivax (eukaryote) / Plasmid: pQE-30 (Qiagen) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: Q9GPQ4, 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.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-AD3 / 3-DEAZA-ADENOSINE


Mass: 266.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM tris, 1.6 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
3100 mMTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2001
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 36763 / Num. obs: 36763 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3372 / % possible all: 95.2
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.349

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: ISOMORPHOUS TO INOSINE COMPLEX, PDB ENTRY 1KIC
Starting model: PDB ENTRY 1KIC

1kic


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1749 4.8 %random
Rwork0.156 ---
all-36763 --
obs-36763 97.3 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 41 604 5515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.85913
X-RAY DIFFRACTIONc_bond_d0.010125
Refinement
*PLUS
Rfactor obs: 0.1564 / Rfactor Rfree: 0.2153 / Rfactor Rwork: 0.1564
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0101
X-RAY DIFFRACTIONc_angle_deg1.859

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