[English] 日本語
Yorodumi
- PDB-2byt: Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2byt
TitleThermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation
Components
  • LEUCYL-TRNA SYNTHETASE
  • TRNALEU TRANSCRIPT WITH ANTICODON CAG
KeywordsSYNTHETASE / AMINOACYL-TRNA SYNTHETASE / ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI L-LEUCYL-TRNA(LEU) / CLASS I AMINOACYL-TRNA SYNTHETASE / EDITING
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucine-tRNA synthetase-specific domain / 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 ...Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucyl-tRNA synthetase, domain 3 / Leucine-tRNA synthetase-specific domain / 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 / Isoleucyl-tRNA Synthetase; Domain 1 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Ubiquitin-like (UB roll) / 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 speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCusack, S. / Tukalo, M. / Yaremchuk, A. / Fukunaga, R. / Yokoyama, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer-Editing Conformation.
Authors: Tukalo, M. / Yaremchuk, A. / Fukunaga, R. / Yokoyama, S. / Cusack, S.
History
DepositionAug 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LEUCYL-TRNA SYNTHETASE
B: TRNALEU TRANSCRIPT WITH ANTICODON CAG
D: LEUCYL-TRNA SYNTHETASE
E: TRNALEU TRANSCRIPT WITH ANTICODON CAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,50227
Polymers256,1364
Non-polymers2,36623
Water0
1
A: LEUCYL-TRNA SYNTHETASE
B: TRNALEU TRANSCRIPT WITH ANTICODON CAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,39515
Polymers128,0682
Non-polymers1,32713
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: LEUCYL-TRNA SYNTHETASE
E: TRNALEU TRANSCRIPT WITH ANTICODON CAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,10712
Polymers128,0682
Non-polymers1,03910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)203.869, 125.578, 172.979
Angle α, β, γ (deg.)90.00, 118.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.561636, -0.027193, 0.826937), (-0.006498, -0.999574, -0.028456), (0.827359, 0.010608, -0.561574)
Vector: -16.038, 61.421, 34.312)
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

-
Components

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

#1: Protein LEUCYL-TRNA SYNTHETASE /


Mass: 101170.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIE4
#2: RNA chain TRNALEU TRANSCRIPT WITH ANTICODON CAG


Mass: 26898.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria)

-
Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4

-
Details

Compound detailsATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI L-LEUCYL-TRNA(LEU)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68 %
Crystal growpH: 7.5
Details: 5MG/ML LEUCYL-TRNA SYNTHETASE MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5 MM L-LEUCINE 15MM MGCL2 50MM MES PH6.5 0.8M AMMONIUM SULPHATE AGAINST RESERVOIR CONTAINING 1.5M AMMONIUM SULPHATE AND 0.1M MES PH6.5, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→25 Å / Num. obs: 57205 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 110.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 3.3→4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 7.33 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3N

1h3n


Resolution: 3.3→24.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 805614706.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2289 4 %RANDOM
Rwork0.243 ---
obs0.243 57205 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5184 Å2 / ksol: 0.230716 e/Å3
Displacement parametersBiso mean: 85.5 Å2
Baniso -1Baniso -2Baniso -3
1-29.68 Å20 Å229.38 Å2
2---18.97 Å20 Å2
3----10.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.3→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14244 3354 99 0 17697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it3.073
X-RAY DIFFRACTIONc_scangle_it4.854
LS refinement shellResolution: 3.29→3.5 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 350 4 %
Rwork0.33 8395 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

+
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