[English] 日本語
Yorodumi
- PDB-4arc: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4arc
TitleTernary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucine in the editing conformation
Components
  • LEUCINE--TRNA LIGASE
  • TRNA-LEU5 (UAA ISOACCEPTOR)
KeywordsLIGASE/RNA / LIGASE-RNA COMPLEX / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / METAL-BINDING
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
Rubrerythrin, domain 2 - #290 / Ubiquitin-like (UB roll) - #590 / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) ...Rubrerythrin, domain 2 - #290 / Ubiquitin-like (UB roll) - #590 / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / 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 / Rubrerythrin, domain 2 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Single Sheet / Rossmann-like alpha/beta/alpha sandwich fold / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LEUCINE / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPalencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase
Authors: Palencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S.
History
DepositionApr 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LEUCINE--TRNA LIGASE
B: TRNA-LEU5 (UAA ISOACCEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7244
Polymers127,5692
Non-polymers1552
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint1.7 kcal/mol
Surface area54930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.080, 119.370, 141.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein LEUCINE--TRNA LIGASE / LEUCYL-TRNA SYNTHETASE / LEURS


Mass: 99516.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain TRNA-LEU5 (UAA ISOACCEPTOR)


Mass: 28052.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNMODIFIED T7 TRANSCRIPT / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growpH: 5.6
Details: THE TERNARY COMPLEX ECLEURS-TRNA-LEU WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 200 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ...Details: THE TERNARY COMPLEX ECLEURS-TRNA-LEU WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 200 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ETHYLENE GLYCOL AS CRYOPROTECTANT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 87917 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 2→45.57 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.325 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 4411 5 %RANDOM
Rwork0.20988 ---
obs0.21229 83506 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.403 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 1516 10 415 8406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0188318
X-RAY DIFFRACTIONr_bond_other_d0.0010.025155
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.84111626
X-RAY DIFFRACTIONr_angle_other_deg1.058312554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76724.476315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.253151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0191538
X-RAY DIFFRACTIONr_chiral_restr0.1020.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021731
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 315 -
Rwork0.337 5761 -
obs--99.09 %

+
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