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- PDB-3epw: Crystal structure of Trypanosoma vivax nucleoside hydrolase in co... -

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Basic information

Entry
Database: PDB / ID: 3epw
TitleCrystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidin-3,4-diol
ComponentsIAG-nucleoside hydrolase
KeywordsHYDROLASE / Rossmann fold / active site loops / aromatic stacking
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
Chem-JMQ / IAG-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma vivax (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVersees, W. / Goeminne, A. / Berg, M. / Vandemeulebroucke, A. / Haemers, A. / Augustyns, K. / Steyaert, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors.
Authors: Versees, W. / Goeminne, A. / Berg, M. / Vandemeulebroucke, A. / Haemers, A. / Augustyns, K. / Steyaert, J.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IAG-nucleoside hydrolase
B: IAG-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9338
Polymers75,2442
Non-polymers6896
Water15,097838
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-31 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.449, 73.728, 81.147
Angle α, β, γ (deg.)90.00, 75.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IAG-nucleoside hydrolase


Mass: 37621.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma vivax (eukaryote) / Plasmid: pQE-30 / 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-JMQ / 7-(((2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl)methyl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one


Mass: 280.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N4O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25 % PEG3350, 0.1 M Bis-Tris, 0.2 M MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8051 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2007
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8051 Å / Relative weight: 1
ReflectionResolution: 1.3→26.86 Å / Num. all: 138694 / Num. obs: 138694 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HOZ (with flexible parts removed)

1hoz


Resolution: 1.3→26.86 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.183 6922 RANDOM (same set of reflections as for PDB entry 1HOZ)
Rwork0.165 --
all0.165 131766 -
obs0.165 131766 -
Refinement stepCycle: LAST / Resolution: 1.3→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 0 44 838 5913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.295
X-RAY DIFFRACTIONr_bond_refined_d0.009

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