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- PDB-1hoz: CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE-PREFERRING NU... -

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Basic information

Entry
Database: PDB / ID: 1hoz
TitleCRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE-PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX
ComponentsINOSINE-ADENOSINE-GUANOSINE-PREFERRING NUCLEOSIDE HYDROLASE
KeywordsHYDROLASE / Rossmann-fold-like motif
Function / homology
Function and homology information


purine nucleosidase activity / 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
IAG-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma vivax (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsVersees, W. / Decanniere, K. / Pelle, R. / Depoorter, J. / Parkin, D.W. / Steyaert, J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax.
Authors: Versees, W. / Decanniere, K. / Pelle, R. / Depoorter, J. / Brosens, E. / Parkin, D.W. / Steyaert, J.
History
DepositionDec 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)76,25512
Polymers75,4382
Non-polymers81710
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-44 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.09, 74.00, 82.00
Angle α, β, γ (deg.)90, 104.56, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein INOSINE-ADENOSINE-GUANOSINE-PREFERRING NUCLEOSIDE HYDROLASE


Mass: 37718.984 Da / Num. of mol.: 2 / Fragment: IAG-NUCLEOSIDE HYDROLASE, IAG-NH
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.03 Å3/Da / Density % sol: 39.31 %
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
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
2100 mMTris1reservoirpH8.5
31.6 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999
RadiationMonochromator: YALE MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8445 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 631096 / Num. obs: 629834 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 629834
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.385

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.21 3989 RANDOM
Rwork0.186 --
all0.186 79329 -
obs0.186 75340 -
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 50 424 5327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_bond_d0.0096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.6-1.610.184890.169X-RAY DIFFRACTION1532
4.86-5.890.184850.169X-RAY DIFFRACTION1544
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.1861 / Rfactor Rfree: 0.2096
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.184 / Rfactor Rwork: 0.169

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