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- PDB-4i73: Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Gua... -

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Basic information

Entry
Database: PDB / ID: 4i73
TitleCrystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with compound UAMC-00312
ComponentsInosine-adenosine-guanosine-nucleoside hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / nucleoside hydrolase / open (alpha / beta) structure / NH fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


purine nucleosidase / purine nucleosidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / glycosome / purine nucleoside catabolic process / purine ribonucleoside salvage / 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
Chem-MBY / NICKEL (II) ION / Inosine-adenosine-guanosine-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGiannese, F. / Degano, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor
Authors: Giannese, F. / Berg, M. / Van der Veken, P. / Castagna, V. / Tornaghi, P. / Augustyns, K. / Degano, M.
#1: Journal: 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.
#2: Journal: Biochemistry / Year: 2010
Title: Structure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei
Authors: Vandemeulebroucke, A. / Minici, C. / Bruno, I. / Muzzolini, L. / Tornaghi, P. / Parkin, D.W. / Versees, W. / Steyaert, J. / Degano, M.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism
Authors: Parkin, D.W.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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-nucleoside hydrolase
B: Inosine-adenosine-guanosine-nucleoside hydrolase
C: Inosine-adenosine-guanosine-nucleoside hydrolase
D: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,01829
Polymers144,6704
Non-polymers2,34725
Water12,070670
1
A: Inosine-adenosine-guanosine-nucleoside hydrolase
C: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,71418
Polymers72,3352
Non-polymers1,37916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-12 kcal/mol
Surface area22670 Å2
MethodPISA
2
B: Inosine-adenosine-guanosine-nucleoside hydrolase
D: Inosine-adenosine-guanosine-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,30311
Polymers72,3352
Non-polymers9689
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-16 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.170, 131.670, 71.850
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32D
13A
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label alt-ID
111THRTHRSERSER1AA4 - 2457 - 248
211THRTHRSERSER1BB4 - 2457 - 248
311THRTHRSERSER1CC4 - 2457 - 248
411THRTHRSERSER1DD4 - 2457 - 248
121TYRTYRMBYMBY1AA - F257 - 402260
221TYRTYRMBYMBY1BB - N257 - 402260
321TYRTYRMBYMBY1CC - R257 - 402260A
421TYRTYRMBYMBY1DD - Z257 - 402260A
112THRTHRALAALA1AA246 - 256249 - 259
212THRTHRALAALA1BB246 - 256249 - 259
312THRTHRALAALA1DD246 - 256249 - 259
113THRTHRALAALA4AA246 - 256249 - 259
213THRTHRALAALA4CC246 - 256249 - 259

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Inosine-adenosine-guanosine-nucleoside hydrolase


Mass: 36167.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.3.2960 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57ZL6, purine nucleosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MBY / (2R,3R,4S)-2-(hydroxymethyl)-1-[(4-hydroxythieno[3,2-d]pyrimidin-7-yl)methyl]pyrrolidine-3,4-diol


Mass: 297.330 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15N3O4S
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMBY C 402 AND NI C 406, MBY D 402 AND NI D 405 PLACE THE ALTERNATE POSITIONS.

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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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.3
Details: 0.1M Tris, 19% PEGMME2000, 10mM Ni2SO4, pH 7.3, Vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2010
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.18→72 Å / Num. all: 61007 / Num. obs: 61007 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.264 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
2.18-2.243.70.830.6711.96160074485437443740.78697.5
2.24-2.30.6950.5882.2716670440043990.686100
2.3-2.360.6250.5222.616243428842830.60999.9
2.36-2.440.5730.4772.8415796416641630.55699.9
2.44-2.520.4840.4033.3815223400640060.47100
2.52-2.60.4030.3453.9414762388338800.40299.9
2.6-2.70.3330.2864.6714378379137860.33499.9
2.7-2.810.3170.2625.1213658358635830.30599.9
2.81-2.940.240.2066.5113291349334910.2499.9
2.94-3.080.20.1757.4312592331633150.204100
3.08-3.250.1510.1369.4612178319331920.158100
3.25-3.450.1030.112.5311321297529730.11699.9
3.45-3.680.0760.07216.0110648281228090.08499.9
3.68-3.980.0680.06517.729948263926350.07699.8
3.98-4.360.050.05321.138996238923890.062100
4.36-4.870.0450.04623.828216220322010.05499.9
4.87-5.630.0520.05121.817193192519210.0699.8
5.63-6.890.050.05321.56121163616340.06199.9
6.89-9.750.0320.03328.64689127712750.03999.8
9.750.0220.02633.8424327116980.03198.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→71.83 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.2237 / WRfactor Rwork: 0.1834 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8361 / SU B: 6.679 / SU ML: 0.171 / SU R Cruickshank DPI: 0.3749 / SU Rfree: 0.2365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 3089 5.1 %RANDOM
Rwork0.2001 ---
obs0.2025 61007 99.72 %-
all-61007 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85.17 Å2 / Biso mean: 23.4422 Å2 / Biso min: 2.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.76 Å2
2---0.55 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.18→71.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9941 0 101 670 10712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210257
X-RAY DIFFRACTIONr_bond_other_d0.0030.026772
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.96613954
X-RAY DIFFRACTIONr_angle_other_deg1.032316661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15725.074406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.147151714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7881535
X-RAY DIFFRACTIONr_chiral_restr0.0890.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111275
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021924
X-RAY DIFFRACTIONr_mcbond_it0.6841.56464
X-RAY DIFFRACTIONr_mcbond_other0.1851.52603
X-RAY DIFFRACTIONr_mcangle_it1.295210460
X-RAY DIFFRACTIONr_scbond_it1.99133793
X-RAY DIFFRACTIONr_scangle_it3.2034.53493
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4011TIGHT POSITIONAL0.050.05
12B4011TIGHT POSITIONAL0.050.05
13C4011TIGHT POSITIONAL0.050.05
14D4011TIGHT POSITIONAL0.050.05
11A4011TIGHT THERMAL0.170.5
12B4011TIGHT THERMAL0.170.5
13C4011TIGHT THERMAL0.20.5
14D4011TIGHT THERMAL0.170.5
21A144TIGHT POSITIONAL0.040.05
22B144TIGHT POSITIONAL0.040.05
23D144TIGHT POSITIONAL0.040.05
21A144TIGHT THERMAL0.180.5
22B144TIGHT THERMAL0.170.5
23D144TIGHT THERMAL0.260.5
31A17MEDIUM POSITIONAL0.120.5
31A17MEDIUM THERMAL2.282
LS refinement shellResolution: 2.179→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 212 -
Rwork0.247 4150 -
all-4362 -
obs--97.41 %

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