[English] 日本語
Yorodumi
- PDB-1qf6: STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qf6
TitleSTRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS COGNATE TRNA
Components
  • THREONINE TRNA
  • THREONYL-TRNA SYNTHETASE
KeywordsLIGASE/RNA / THREONYL-TRNA SYNTHETASE / TRNA(THR) / AMP / MRNA / AMINOACYLATION / TRANSLATIONAL REGULATION / PROTEIN/RNA / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : ...Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Beta-grasp domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / RNA / RNA (> 10) / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å
AuthorsSankaranarayanan, R. / Dock-Bregeon, A.C. / Rees, B. / Moras, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site
Authors: Sankaranarayanan, R. / Dock-Bregeon, A.C. / Romby, P. / Caillet, J. / Springer, M. / Rees, B. / Ehresmann, C. / Ehresmann, B. / Moras, D.
History
DepositionApr 6, 1999Deposition site: PDBE / Processing site: NDB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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
B: THREONINE TRNA
A: THREONYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1684
Polymers98,7552
Non-polymers4132
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.670, 162.670, 128.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

-
Components

#1: RNA chain THREONINE TRNA / TRNA (THR)


Mass: 24634.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPLEXED WITH ADENOSINE MONOPHOSPHATE / Source: (natural) Escherichia coli (E. coli)
#2: Protein THREONYL-TRNA SYNTHETASE / E.C.6.1.1.3 / THRRS


Mass: 74120.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 4.97 Å3/Da / Density % sol: 74 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: AMMONIUM ACETATE, PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1AMMONIUM ACETATE11
2PEG 400011
3AMMONIUM ACETATE12
4PEG 400012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDDetails
1ThrRS1
2tRNAThr1
3ammonium acetate11
4ATP11
5PEG400012precipitant

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.998
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 43094 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.6 Å2 / Rsym value: 0.074 / Net I/σ(I): 16.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.337 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 176615 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.337

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNS0.5refinement
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 2263872.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3118 7.6 %RANDOM
Rwork0.195 ---
obs-41055 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.76 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å213 Å20 Å2
2---0.72 Å20 Å2
3---1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 1633 24 244 7093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 463 7.3 %
Rwork0.291 5862 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_C.PARAMDNA-RNA_D.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4AMD_NEW.PARAMLIGAND_NEW4.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.61

+
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