[English] 日本語
Yorodumi
- PDB-8h9c: Crystal structure of chemically modified E. coli ThrS catalytic d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h9c
TitleCrystal structure of chemically modified E. coli ThrS catalytic domain 4
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like / tRNA synthetase class II core domain (G, H, P, S and T) / TGS domain profile. / TGS / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Chem-X5V / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsQiao, H. / Xia, M. / Wang, J. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: Commun Biol / Year: 2023
Title: Tyrosine-targeted covalent inhibition of a tRNA synthetase aided by zinc ion.
Authors: Qiao, H. / Xia, M. / Cheng, Y. / Zhou, J. / Zheng, L. / Li, W. / Wang, J. / Fang, P.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3633
Polymers47,9221
Non-polymers4422
Water3,405189
1
A: Threonine--tRNA ligase
hetero molecules

A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7276
Polymers95,8432
Non-polymers8834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4070 Å2
ΔGint-20 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.180, 92.180, 120.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-931-

HOH

-
Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 47921.535 Da / Num. of mol.: 1 / Fragment: UNP residues 242-642 / Mutation: Y462R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: E2QMS9, threonine-tRNA ligase
#2: Chemical ChemComp-X5V / N-(2,3-dihydroxybenzoyl)-4-(4-nitrophenyl)-L-threonine


Type: L-peptide NH3 amino terminus / Mass: 376.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C17H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ...Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ethylene glycol, 10% w/v PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 12955 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.778 / Num. unique obs: 2446

-
Processing

Software
NameVersionClassification
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FYF

1fyf


Resolution: 2.15→48.14 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 622 4.8 %
Rwork0.2255 12333 -
obs0.2278 12955 39.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 37.95 Å2 / Biso mean: 18.7157 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 2.15→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 189 3454
Biso mean---16.17 -
Num. residues----399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.370.3015110.36942983094
2.37-2.710.3698620.3031041110314
2.71-3.410.3551640.26773089325340
3.41-48.140.24023850.20247905829098
Refinement TLS params.Method: refined / Origin x: 41.9046 Å / Origin y: 1.374 Å / Origin z: 8.1045 Å
111213212223313233
T0.1042 Å2-0.0518 Å2-0.0215 Å2-0.1535 Å20.0093 Å2---0.0342 Å2
L0.2215 °20.1479 °2-0.0827 °2-0.6747 °20.1801 °2--1.0919 °2
S0.0083 Å °0.0059 Å °0.0311 Å °-0.0215 Å °0.0735 Å °0.0335 Å °-0.0666 Å °-0.0544 Å °0.0437 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA242 - 640
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 203

+
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