[English] 日本語
Yorodumi
- PDB-1r4f: Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r4f
TitleInosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma vivax: Trp260Ala Mutant In Complex With 3-Deaza-Adenosine
ComponentsIAG-nucleoside hydrolase
KeywordsHYDROLASE / Rossmann fold / 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
3-DEAZA-ADENOSINE / IAG-nucleoside hydrolase
Similarity search - Component
Biological speciesTrypanosoma vivax (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous to PDB entry 1HP0 / Resolution: 2.3 Å
AuthorsVersees, W. / Loverix, S. / Vandemeulebroucke, A. / Geerlings, P. / Steyaert, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Leaving group activation by aromatic stacking: an alternative to general Acid catalysis.
Authors: Versees, W. / Loverix, S. / Vandemeulebroucke, A. / Geerlings, P. / Steyaert, J.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE The author states: the correct sequence is ASN 301, the sequence in the database is ...SEQUENCE The author states: the correct sequence is ASN 301, the sequence in the database is probably not correct, which was further confirmed by the original depositor.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IAG-nucleoside hydrolase
B: IAG-nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5545
Polymers75,2082
Non-polymers3463
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-38 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.996, 74.865, 81.369
Angle α, β, γ (deg.)90, 102.291, 90
Int Tables number4
Space group name H-MP1211
DetailsThe assymetric unit contains the biologically relevant homodimer

-
Components

#1: Protein IAG-nucleoside hydrolase


Mass: 37603.852 Da / Num. of mol.: 2 / Fragment: IAG-NH / Mutation: W260A
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-AD3 / 3-DEAZA-ADENOSINE


Mass: 266.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6 M ammonium sulfate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2003
RadiationMonochromator: The undulator radiation is monochromatised using the [111] reflection from thin diamond crystals in Bragg (60micron thick diamond) or Laue mode (150microns thick diamond). Subsequently ...Monochromator: The undulator radiation is monochromatised using the [111] reflection from thin diamond crystals in Bragg (60micron thick diamond) or Laue mode (150microns thick diamond). Subsequently the beam is brought back to parallel with the transmitted beam by a Ge [220] crystal and focused by a toroidal mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 26932 / Num. obs: 26932 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.43 % / Biso Wilson estimate: 27.45 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.29
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.298 / % possible all: 92.3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: isomorphous to PDB entry 1HP0
Starting model: PDB entry 1HP0

1hp0


Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 1318 RANDOM (same set of reflections as for PDB entry 1HP0)
Rwork0.205 --
all0.208 26924 -
obs0.208 26924 -
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 21 163 4927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34993
X-RAY DIFFRACTIONc_bond_d0.006478
LS refinement shellResolution: 2.3→2.33 Å /
RfactorNum. reflection
Rfree0.31 46
Rwork0.3 -
obs-973

+
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