[English] 日本語
Yorodumi
- PDB-6i5y: Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i5y
TitleCrystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-adenosine
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / Rossmann fold / tRNA aminoacylation
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain / RNA-binding S4 domain ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile.
Similarity search - Domain/homology
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders1S53518N Belgium
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.
Authors: Nautiyal, M. / De Graef, S. / Pang, L. / Gadakh, B. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Category: pdbx_database_proc
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3957
Polymers95,1902
Non-polymers1,2055
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-12 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.393, 66.508, 91.710
Angle α, β, γ (deg.)90.000, 101.730, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 47594.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: tyrS, ECBD_2006 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A140NBN7, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were ...Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were transferred to a drop containing mother liquor supplemented with 2 mM inhibitor.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979292 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2018
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979292 Å / Relative weight: 1
ReflectionResolution: 1.8→79.7 Å / Num. obs: 87607 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.93.60.878126200.7460.5341.02997.7
5.69-79.73.50.04929220.9950.030.05899.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUD

4oud


Resolution: 1.9→79.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2239 3 %RANDOM
Rwork0.193 ---
obs0.194 74654 98.5 %-
Displacement parametersBiso max: 140.93 Å2 / Biso mean: 42.52 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.8606 Å20 Å20.1504 Å2
2---9.455 Å20 Å2
3---2.5944 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.9→79.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 0 82 734 7230
Biso mean--34.16 51.89 -
Num. residues----826
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2282SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes188HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1005HARMONIC5
X-RAY DIFFRACTIONt_it6631HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion854SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8267SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6631HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8986HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion15.86
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2352 167 3.05 %
Rwork0.2077 5306 -
all0.2085 5473 -
obs--97.62 %
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)
10.9075-0.01510.65590.62340.05552.3719-0.03270.0397-0.03380.0162-0.0061-0.0061-0.0699-0.03980.03870.22980.00230.00340.1324-0.01610.2072-38.68161.7356-9.3766
22.9427-0.8211-0.04631.28590.34362.298-0.1196-0.19590.19310.06040.0224-0.1699-0.19110.29360.09720.214-0.0172-0.03870.2152-0.00140.2103-17.28617.63068.0907
37.39410.4921-1.74710.37990.26211.74250.0672-0.2090.2080.04250.1533-0.0053-0.14320.1547-0.22050.27180.03250.03930.3668-0.03480.36539.40954.5751-2.7002
41.3706-0.09630.7730.8553-0.32712.22050.00030.22910.0154-0.04790.02850.03970.0216-0.0322-0.02880.2026-0.010.00880.3041-0.01140.1986-48.6650.5854-45.0727
52.23850.2276-0.23991.111-0.22660.9077-0.02280.31680.2634-0.0053-0.1049-0.0044-0.23510.06530.12780.24660.0041-0.01040.35850.01590.2421-44.22236.7268-48.4737
62.56040.92790.13161.5609-0.58090.9635-0.061-0.15810.22720.051-0.01860.0396-0.194-0.35090.07960.22920.0269-0.02760.54080.03110.2868-71.49185.4683-55.0021
73.08910.053-0.28920.2612-0.2595-0.25330.0835-0.2242-0.08810.0882-0.05350.0524-0.08780.1206-0.030.2517-0.02240.00590.54860.03930.2179-85.27315.4588-58.2168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|5 - B|235 }B5 - 235
2X-RAY DIFFRACTION2{ B|236 - B|329 }B236 - 329
3X-RAY DIFFRACTION3{ B|330 - B|424 }B330 - 424
4X-RAY DIFFRACTION4{ A|5 - A|191 }A5 - 191
5X-RAY DIFFRACTION5{ A|192 - A|235 }A192 - 235
6X-RAY DIFFRACTION6{ A|236 - A|264 }A236 - 264
7X-RAY DIFFRACTION7{ A|265 - A|424 }A265 - 424

+
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