[English] 日本語
Yorodumi
- PDB-2v0g: LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v0g
TitleLEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A tRNA(leu) transcript with 5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1- BENZOXABOROLE (AN2690) forming an adduct to the ribose of adenosine- 76 in the enzyme editing site.
Components
  • AMINOACYL-TRNA SYNTHETASEAminoacyl tRNA synthetase
  • TRNALEU
KeywordsLIGASE / CLASS I AMINOACYL- TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / AMINOACYL-TRNA SYNTHETASE / ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI L-LEUCYL-TRNA SYNTHETASE / METAL-BINDING / NUCLEOTIDE-BINDING ZINC / EDITING / SYNTHETASE / ATP-BINDING
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: 3.5 Å
AuthorsRock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. ...Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / Cusack, S. / Alley, M.R.K.
CitationJournal: Science / Year: 2007
Title: An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site.
Authors: Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / ...Authors: Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / Cusack, S. / Alley, M.R.K.
History
DepositionMay 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMINOACYL-TRNA SYNTHETASE
B: TRNALEU
D: AMINOACYL-TRNA SYNTHETASE
F: TRNALEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,28822
Polymers256,4024
Non-polymers1,88618
Water0
1
A: AMINOACYL-TRNA SYNTHETASE
B: TRNALEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,33613
Polymers128,2012
Non-polymers1,13511
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: AMINOACYL-TRNA SYNTHETASE
F: TRNALEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9529
Polymers128,2012
Non-polymers7517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)202.050, 125.800, 173.200
Angle α, β, γ (deg.)90.00, 118.71, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.548828, -0.019476, 0.835708), (-0.005341, -0.99979, -0.019793), (0.835918, 0.006399, -0.548817)
Vector: 19.7189, 47.7446, -33.8051)

-
Components

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

#1: Protein AMINOACYL-TRNA SYNTHETASE / Aminoacyl tRNA synthetase / 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) / Strain: HB-27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIE4
#2: RNA chain TRNALEU


Mass: 27030.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TRNALEU TRANSCRIPT WITH ANTICODON CAG / Source: (synth.) THERMUS THERMOPHILUS (bacteria)

-
Non-polymers , 4 types, 18 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.: 10 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68 %
Crystal growDetails: 5MG/ML LEUCYL-TRNA SYNTHETASE, MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5MM 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 138057 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.69 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYT

2byt


Resolution: 3.5→152.5 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.817 / SU B: 39.399 / SU ML: 0.629 / Cross valid method: THROUGHOUT / ESU R Free: 0.724 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 2324 5.1 %RANDOM
Rwork0.245 ---
obs0.249 43437 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.29 Å2
Baniso -1Baniso -2Baniso -3
1-12.08 Å20 Å27.82 Å2
2---4.06 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 3.5→152.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14244 3286 74 0 17604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211588
X-RAY DIFFRACTIONr_angle_refined_deg1.3352.19625696
X-RAY DIFFRACTIONr_angle_other_deg0.873328258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51651750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06723.201706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.442152494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.45615122
X-RAY DIFFRACTIONr_chiral_restr0.0790.22836
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023114
X-RAY DIFFRACTIONr_nbd_refined0.2120.24481
X-RAY DIFFRACTIONr_nbd_other0.1870.212769
X-RAY DIFFRACTIONr_nbtor_refined0.1970.28013
X-RAY DIFFRACTIONr_nbtor_other0.0850.28580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1610.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6691.511330
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.715214142
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.682312562
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3494.511554
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: 3.5→3.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 176
Rwork0.321 3259

+
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