[English] 日本語
Yorodumi
- PDB-5on2: Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5on2
TitleQuaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline in the aminoacylation conformation
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsTRANSLATION / reaction catalysed: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) protein translation / aminoacyl-tRNA activity / leucine-tRNA ligase / class Ia
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / 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
Similarity search - Domain/homology
5'-O-(L-leucylsulfamoyl)adenosine / 2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPalencia, A. / Cusack, S.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Authors: Dulic, M. / Cvetesic, N. / Zivkovic, I. / Palencia, A. / Cusack, S. / Bertosa, B. / Gruic-Sovulj, I.
History
DepositionAug 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 17, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine--tRNA ligase
B: tRNA(leu)
D: Leucine--tRNA ligase
E: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,90612
Polymers255,0774
Non-polymers1,8298
Water00
1
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4536
Polymers127,5392
Non-polymers9154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-96 kcal/mol
Surface area48320 Å2
MethodPISA
2
D: Leucine--tRNA ligase
E: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4536
Polymers127,5392
Non-polymers9154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-58 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.650, 70.620, 230.340
Angle α, β, γ (deg.)90.00, 104.52, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / RNA chain , 2 types, 4 molecules ADBE

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 99485.992 Da / Num. of mol.: 2 / Mutation: T252A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: leuS, b0642, JW0637 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 28052.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: T7 in vitro transcription / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1231762938

-
Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S
#5: Chemical ChemComp-VRT / 2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE


Mass: 365.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.45 % / Description: 2d needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 45457 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rsym value: 0.01 / Net I/σ(I): 6.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4483 / CC1/2: 0.29 / Rsym value: 1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AQ7

4aq7


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 33.259 / SU ML: 0.524 / Cross valid method: THROUGHOUT / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26316 2193 4.8 %RANDOM
Rwork0.22578 ---
obs0.22757 43264 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.831 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-1.33 Å2
2--0.18 Å2-0 Å2
3---0.67 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13676 3538 118 0 17332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01818077
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214535
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.79325341
X-RAY DIFFRACTIONr_angle_other_deg0.899333897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9951720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87224.551668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19152380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6081582
X-RAY DIFFRACTIONr_chiral_restr0.0530.22742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02117695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5529.756898
X-RAY DIFFRACTIONr_mcbond_other1.5529.756898
X-RAY DIFFRACTIONr_mcangle_it2.84714.6258612
X-RAY DIFFRACTIONr_mcangle_other2.84714.6258613
X-RAY DIFFRACTIONr_scbond_it1.14510.00711179
X-RAY DIFFRACTIONr_scbond_other1.14510.00711180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.07915.01716730
X-RAY DIFFRACTIONr_long_range_B_refined4.3120286
X-RAY DIFFRACTIONr_long_range_B_other4.3120287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 148 -
Rwork0.373 3170 -
obs--99.91 %

+
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