[English] 日本語
Yorodumi
- PDB-3fz0: Inosine-Guanosine Nucleoside Hydrolase (IG-NH) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fz0
TitleInosine-Guanosine Nucleoside Hydrolase (IG-NH)
ComponentsNucleoside hydrolase, putative
KeywordsHYDROLASE / NH fold / open alpha/beta structure / Glycosidase
Function / homology
Function and homology information


guanosine salvage / inosine nucleosidase activity / inosine salvage / purine nucleosidase / glycosome / metal ion binding / cytoplasm
Similarity search - Function
Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nucleoside hydrolase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVandemeulebroucke, A. / Minici, C. / Bruno, I. / Muzzolini, L. / Tornaghi, P. / Parkin, D.W. / Schramm, V.L. / Versees, W. / Steyaert, J. / Degano, M.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Guanosine-inosine-preferring nucleoside N-glycohydrolase from Crithidia fasciculata
Authors: Estupinan, B. / Schramm, V.L.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / pdbx_initial_refinement_model / 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_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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside hydrolase, putative
B: Nucleoside hydrolase, putative
C: Nucleoside hydrolase, putative
D: Nucleoside hydrolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,73712
Polymers158,7394
Non-polymers9978
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-66 kcal/mol
Surface area47790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.690, 116.040, 204.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22C
32D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISALAALAAA3 - 1186 - 121
211HISHISALAALABB3 - 1186 - 121
311HISHISALAALACC3 - 1186 - 121
411HISHISALAALADD3 - 1186 - 121
121TYRTYRLEULEUAA126 - 221129 - 224
221TYRTYRLEULEUBB126 - 221129 - 224
321TYRTYRLEULEUCC126 - 221129 - 224
421TYRTYRLEULEUDD126 - 221129 - 224
131GLNGLNCYSCYSAA240 - 315243 - 318
231GLNGLNCYSCYSBB240 - 315243 - 318
331GLNGLNCYSCYSCC240 - 315243 - 318
431GLNGLNCYSCYSDD240 - 315243 - 318
141ASNASNALAALAAA333 - 357336 - 360
241ASNASNALAALABB333 - 357336 - 360
341ASNASNALAALACC333 - 357336 - 360
441ASNASNALAALADD333 - 357336 - 360
112GLUGLUVALVALAA119 - 125122 - 128
212GLUGLUVALVALCC119 - 125122 - 128
312GLUGLUVALVALDD119 - 125122 - 128

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Nucleoside hydrolase, putative / Inosine-Guanosine-preferring Nucleoside Hydrolase


Mass: 39684.824 Da / Num. of mol.: 4 / Mutation: K97E, L226S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.7.4570 / Plasmid: pET28-ignh / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q57X73, 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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 200mM ammonium sulfate, 22% PEG MME 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97565 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 2.5→85.13 Å / Num. obs: 51751 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 43.5 Å2 / Rsym value: 0.118 / Net I/σ(I): 16.1 / Num. measured all: 374972
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 7263 / Rsym value: 0.546 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q8F

1q8f


Resolution: 2.5→19.93 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.805 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.619 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; These residues listed in remark 500: COVALENT BOND LENGTHS are close to a very flexible region that was not included in the model. Since ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; These residues listed in remark 500: COVALENT BOND LENGTHS are close to a very flexible region that was not included in the model. Since weak difference density is present, this might lead to a distortion of the bonds and angles. The amino acid fit reasonably the electron density, and are kept in the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.22433 2620 5.1 %RANDOM
Rwork0.1892 ---
obs0.19102 48811 99.9 %-
all-48811 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10272 0 60 186 10518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.95514455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34351332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42824.746493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.505151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7121565
X-RAY DIFFRACTIONr_chiral_restr0.0990.21636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.24875
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.27261
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2382
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.56777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.949210668
X-RAY DIFFRACTIONr_scbond_it1.54734409
X-RAY DIFFRACTIONr_scangle_it2.4584.53775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2216tight positional0.050.05
12B2216tight positional0.050.05
13C2216tight positional0.050.05
14D2216tight positional0.050.05
21A52tight positional0.120.05
22C52tight positional0.140.05
23D52tight positional0.050.05
11A2216tight thermal0.120.5
12B2216tight thermal0.130.5
13C2216tight thermal0.120.5
14D2216tight thermal0.110.5
21A52tight thermal0.130.5
22C52tight thermal0.140.5
23D52tight thermal0.080.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 211 -
Rwork0.265 3451 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9971-0.45390.61381.7399-0.34141.67030.02420.0528-0.1145-0.1143-0.04820.18340.1209-0.11410.024-0.27830.0510.0957-0.24150.1294-0.2687-13.502837.824-28.2904
21.6813-0.40880.40871.6821-0.89221.53440.12570.09770.1574-0.0357-0.2008-0.18850.12860.07030.0751-0.2870.06330.0903-0.27830.1211-0.26522.784918.7563-14.7309
32.5234-0.8843-0.1991.9387-0.49551.8957-0.1792-0.34990.11740.29550.1183-0.0768-0.46720.06050.0609-0.12710.07310.0862-0.26790.0683-0.32317.425172.1322-28.9616
42.7892-0.1871-1.21652.2748-0.30362.6122-0.1558-0.299-0.2984-0.1253-0.1192-0.5850.01530.59150.275-0.29010.08020.1664-0.10570.24450.020241.431347.6352-36.9575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 357
2X-RAY DIFFRACTION2B2 - 357
3X-RAY DIFFRACTION3C2 - 357
4X-RAY DIFFRACTION4D3 - 357

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more