[English] 日本語
Yorodumi
- PDB-8brw: Escherichia coli methionyl-tRNA synthetase mutant L13C,I297C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8brw
TitleEscherichia coli methionyl-tRNA synthetase mutant L13C,I297C
ComponentsMethionine--tRNA ligase
KeywordsTRANSLATION / beta-methionine / aminoacyl-tRNA synthetase / MetRS / tRNA
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. ...Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSchmitt, E. / Mechulam, Y. / Nigro, G. / Opuu, V. / Lazennec-Schurdevin, C. / Simonson, T.
Funding support France, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)UMR7654 France
Other governmentUMR7654
CitationJournal: Protein Sci. / Year: 2023
Title: Redesigning methionyl-tRNA synthetase for beta-methionine activity with adaptive landscape flattening and experiments.
Authors: Opuu, V. / Nigro, G. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E. / Simonson, T.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7752
Polymers64,7101
Non-polymers651
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.810, 45.580, 86.470
Angle α, β, γ (deg.)90.000, 107.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 64709.977 Da / Num. of mol.: 1 / Mutation: L13C, I297C, E548Stop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metG, b2114, JW2101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00959, methionine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.08M ammonium citrate, 30 mM potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 60237 / % possible obs: 97.3 % / Redundancy: 6 % / Biso Wilson estimate: 21.75 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.17 / Rsym value: 0.155 / Net I/σ(I): 8.1
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 8415 / CC1/2: 0.526 / Rrim(I) all: 1.305 / Rsym value: 1.179 / % possible all: 84.3

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9C

3h9c


Resolution: 1.73→48.77 Å / SU ML: 0.1948 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.4811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 3053 5.07 %
Rwork0.1686 57108 -
obs0.1705 60161 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.17 Å2
Refinement stepCycle: LAST / Resolution: 1.73→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4371 0 1 620 4992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744522
X-RAY DIFFRACTIONf_angle_d0.82296126
X-RAY DIFFRACTIONf_chiral_restr0.052639
X-RAY DIFFRACTIONf_plane_restr0.0083801
X-RAY DIFFRACTIONf_dihedral_angle_d13.23321659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.760.312640.28111158X-RAY DIFFRACTION42.91
1.76-1.780.29851230.25552639X-RAY DIFFRACTION99.86
1.78-1.810.25291610.24352624X-RAY DIFFRACTION99.89
1.81-1.850.2991440.24492646X-RAY DIFFRACTION99.93
1.85-1.880.30191350.24832663X-RAY DIFFRACTION100
1.88-1.920.29991310.25162653X-RAY DIFFRACTION99.96
1.92-1.960.27061390.23272659X-RAY DIFFRACTION99.96
1.96-2.010.29441270.20882626X-RAY DIFFRACTION99.96
2.01-2.060.22861500.19122659X-RAY DIFFRACTION100
2.06-2.120.22611320.18222644X-RAY DIFFRACTION99.96
2.12-2.180.20921340.17462676X-RAY DIFFRACTION99.75
2.18-2.250.22911490.17662628X-RAY DIFFRACTION99.86
2.25-2.330.23031320.17822674X-RAY DIFFRACTION99.79
2.33-2.420.20261340.17042664X-RAY DIFFRACTION99.71
2.42-2.530.24281540.16692642X-RAY DIFFRACTION99.36
2.53-2.660.21941570.16472644X-RAY DIFFRACTION99.96
2.66-2.830.19831580.1612665X-RAY DIFFRACTION100
2.83-3.050.19971430.15942685X-RAY DIFFRACTION99.96
3.05-3.360.20431600.15092640X-RAY DIFFRACTION99.82
3.36-3.840.15231320.13812703X-RAY DIFFRACTION99.93
3.84-4.840.13821480.12492718X-RAY DIFFRACTION100
4.84-48.770.1851460.16322798X-RAY DIFFRACTION99.7

+
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