[English] 日本語
Yorodumi
- PDB-8db9: Adenosine/guanosine nucleoside hydrolase bound to inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8db9
TitleAdenosine/guanosine nucleoside hydrolase bound to inhibitor
ComponentsInosine-uridine preferring nucleoside hydrolase family protein
KeywordsHYDROLASE/HYDROLASE inhibitor / Nucleoside / Hydrolase / Adenosine / Guanosine / Parasitic / Inhibitor / HYDROLASE-HYDROLASE inhibitor complex
Function / homologypurine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / purine nucleoside catabolic process / metal ion binding / cytosol / Chem-R1Y / Inosine-uridine preferring nucleoside hydrolase family protein
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsMuellers, S.N. / Allen, K.N. / Stockman, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI128585 United States
CitationJournal: Biochemistry / Year: 2022
Title: Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase.
Authors: Muellers, S.N. / Nyitray, M.M. / Reynarowych, N. / Saljanin, E. / Benzie, A.L. / Schoenfeld, A.R. / Stockman, B.J. / Allen, K.N.
History
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
C: Inosine-uridine preferring nucleoside hydrolase family protein
D: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,79511
Polymers133,9054
Non-polymers8907
Water00
1
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
C: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules

D: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,79511
Polymers133,9054
Non-polymers8907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4890 Å2
ΔGint-49 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.406, 75.382, 88.856
Angle α, β, γ (deg.)65.466, 80.791, 87.323
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
Inosine-uridine preferring nucleoside hydrolase family protein


Mass: 33476.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_213720 / Production host: Escherichia coli (E. coli) / References: UniProt: A2EYV3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-R1Y / 1-beta-D-ribofuranosyl-1H-1,2,4-triazole-3-carboximidamide


Mass: 243.220 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H13N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 25% PEG-3350, and 0.1 M Bis-tris, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.89→38.13 Å / Num. obs: 23552 / % possible obs: 87.89 % / Redundancy: 4.2 % / Biso Wilson estimate: 61.28 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.105 / Rrim(I) all: 0.22 / Net I/σ(I): 6.9
Reflection shellResolution: 2.89→2.993 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2425 / CC1/2: 0.408 / Rpim(I) all: 0.738 / Rrim(I) all: 0.149 / % possible all: 88.09

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2.89→38.13 Å / SU ML: 0.587 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 39.3732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3411 1358 5.87 %
Rwork0.2604 21787 -
obs0.265 23145 88.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.8 Å2
Refinement stepCycle: LAST / Resolution: 2.89→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 55 0 9407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01059600
X-RAY DIFFRACTIONf_angle_d1.252713053
X-RAY DIFFRACTIONf_chiral_restr0.07081484
X-RAY DIFFRACTIONf_plane_restr0.00671705
X-RAY DIFFRACTIONf_dihedral_angle_d23.22693498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.990.41751300.34592207X-RAY DIFFRACTION88.09
2.99-3.110.41551400.34782111X-RAY DIFFRACTION87.08
3.11-3.250.38181350.32382203X-RAY DIFFRACTION88.69
3.25-3.430.39321300.33882099X-RAY DIFFRACTION84.08
3.43-3.640.44991330.33452168X-RAY DIFFRACTION87.79
3.64-3.920.39851340.30892111X-RAY DIFFRACTION85.3
3.92-4.320.35021340.24792162X-RAY DIFFRACTION87.77
4.32-4.940.28281410.21632267X-RAY DIFFRACTION90.73
4.94-6.220.3421380.24532220X-RAY DIFFRACTION90.17
6.22-38.130.24111430.17322239X-RAY DIFFRACTION90.78

+
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://pdbjlvh1.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