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- PDB-2ff2: Crystal structure of Trypanosoma vivax nucleoside hydrolase co-cr... -

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Basic information

Entry
Database: PDB / ID: 2ff2
TitleCrystal structure of Trypanosoma vivax nucleoside hydrolase co-crystallized with ImmucillinH
ComponentsIAG-nucleoside hydrolase
KeywordsHYDROLASE / Rossmann fold / loop ordering / 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-IMH / NICKEL (II) ION / IAG-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma vivax (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVersees, W. / Barlow, J. / Steyaert, J.
CitationJournal: 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.
History
DepositionDec 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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_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 1.4Sep 20, 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: IAG-nucleoside hydrolase
B: IAG-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1097
Polymers75,4382
Non-polymers6715
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-57 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.19, 74.39, 73.96
Angle α, β, γ (deg.)90, 98.38, 90
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the biologically relevant homodimer

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Components

#1: Protein IAG-nucleoside hydrolase


Mass: 37718.984 Da / Num. of mol.: 2 / Fragment: IAG-NH
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


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


Mass: 18.015 Da / Num. of mol.: 444 / 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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6 M ammonium sulphate, 100 mM Tris pH 8.5, 215 microM Immucillin H , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8131 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2005
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8131 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 31456 / Num. obs: 31456 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 15.17 Å2 / Rmerge(I) obs: 0.218 / Net I/σ(I): 9.12
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.08 / Num. unique all: 3157 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1HOZ

1hoz


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 1502 RANDOM
Rwork0.167 --
all0.167 29666 -
obs0.167 29649 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 41 444 5490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.43875
X-RAY DIFFRACTIONc_bond_d0.007908
LS refinement shellResolution: 2.2→2.23 Å
RfactorNum. reflection
Rfree0.305 60
Rwork0.2319 -
obs-1006

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