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- PDB-3b9g: Crystal structure of loop deletion mutant of Trypanosoma vivax nu... -

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Basic information

Entry
Database: PDB / ID: 3b9g
TitleCrystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH
ComponentsIAG-nucleoside hydrolase
KeywordsHYDROLASE / Rossmann fold / Flexible loop deletion / Transition state complex
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 / IAG-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma vivax (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVandemeulebroucke, A. / De Vos, S. / Van Holsbeke, E. / Steyaert, J. / Versees, W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax.
Authors: Vandemeulebroucke, A. / De Vos, S. / Van Holsbeke, E. / Steyaert, J. / Versees, W.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _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
Remark 999deleted loop C245-Y257 replaced by linker G245-G247

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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)73,2907
Polymers72,6552
Non-polymers6365
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.177, 74.881, 72.424
Angle α, β, γ (deg.)90.00, 98.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IAG-nucleoside hydrolase


Mass: 36327.422 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 632 / 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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 4000, 10mM sodium acetate, 0.25M ammonium sulfate, 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: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 25, 2007
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.4→40.32 Å / Num. obs: 112485 / % possible obs: 99.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 17.262 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.98
Reflection shellResolution: 1.4→1.436 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.27 / Num. unique all: 7821 / % possible all: 99.73

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHASERphasing
REFMAC5refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HOZ

1hoz


Resolution: 1.4→40.32 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.204 5566 same set of reflections as for PDB 1HOZ
Rwork0.177 --
all0.177 --
obs0.177 106919 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.39 Å2
2---0.9 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 79 632 5668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.252
X-RAY DIFFRACTIONr_bond_refined_d0.008
LS refinement shellResolution: 1.4→1.436 Å
RfactorNum. reflection
Rfree0.304 432
Rwork0.271 -
obs-7821

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