[English] 日本語
Yorodumi
- PDB-6l2q: Threonyl-tRNA synthetase from Salmonella enterica in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l2q
TitleThreonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / tRNA synthetase / drug target / homodimer
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
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. ...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 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E4O / Threonine--tRNA ligase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuo, J. / Chen, B. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Discovery of novel tRNA-amino acid dual-site inhibitors against threonyl-tRNA synthetase by fragment-based target hopping.
Authors: Guo, J. / Chen, B. / Yu, Y. / Cheng, B. / Cheng, Y. / Ju, Y. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionOct 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Threonine--tRNA ligase
B: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8927
Polymers95,9292
Non-polymers9635
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-20 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.231, 101.917, 105.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 47964.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
Gene: thrS, A628_05061 / Production host: Escherichia coli (E. coli) / References: UniProt: V7II86, threonine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E4O / (2S,3R)-2-azanyl-N-[(E)-4-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]but-2-enyl]-3-oxidanyl-butanamide


Mass: 385.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18Cl2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 0.22 M lithium acetate pH 7.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.3→22.18 Å / Num. obs: 41697 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 6025 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWP

4hwp


Resolution: 2.3→22.18 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.862 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.252
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 2147 5.2 %RANDOM
Rwork0.2094 ---
obs0.2117 39447 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.92 Å2 / Biso mean: 30.339 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å2-0 Å20 Å2
2---1.57 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 2.3→22.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6501 0 56 435 6992
Biso mean--25.75 27.65 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196728
X-RAY DIFFRACTIONr_bond_other_d0.0060.026293
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9429079
X-RAY DIFFRACTIONr_angle_other_deg0.883314438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94523.58352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.782151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4621562
X-RAY DIFFRACTIONr_chiral_restr0.0620.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021646
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 164 -
Rwork0.287 2874 -
all-3038 -
obs--99.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1446-0.0089-0.1750.2458-0.18560.3892-0.0113-0.02320.0016-0.00410.01670.0337-0.0010.0556-0.00540.131-0.0195-0.03880.0853-0.00780.07724.4363-0.386-10.3741
20.1697-0.1933-0.10920.3877-0.00340.2729-0.0036-0.0025-0.00360.02760.05720.0814-0.00560.0533-0.05360.11420.00130.03440.1010.00770.0825-10.83514.709-2.3667
30.1194-0.1332-0.01010.39520.02490.009-0.0121-0.00410.00520.0240.03460.03160.01830.0105-0.02250.1630.03270.00230.08890.00070.0536-3.4453-9.5963-4.6193
40.4064-0.4962-0.06122.70990.60490.1457-0.13960.06560.00740.24940.11720.11720.06360.04630.02240.20940.0221-0.00680.0380.01140.00834.1249-33.9602-1.9541
50.0922-0.03080.00090.221-0.16080.1368-0.056-0.0570.0172-0.0360.0534-0.04460.0152-0.04040.00260.14350.0033-0.00270.0883-0.01880.07994.5451-4.0127-25.2325
60.1326-0.118-0.1380.12690.13740.1743-0.0322-0.01590.0198-0.02710.0271-0.0345-0.01270.04460.00520.1339-0.03250.01790.1019-0.00930.107118.1437-11.596-29.8377
70.4256-0.0470.07810.07170.03610.05780.0313-0.1247-0.0172-0.0950.0176-0.0237-0.0455-0.0367-0.0490.1424-0.0150.00440.09730.01520.0769-3.6802-13.1385-28.6507
82.34190.6137-0.36230.19920.06080.8282-0.04430.1827-0.1293-0.00650.0676-0.05070.0962-0.1721-0.02330.0756-0.0696-0.04470.13410.03390.0669-21.8467-22.2088-30.7309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A241 - 333
2X-RAY DIFFRACTION2A334 - 464
3X-RAY DIFFRACTION3A465 - 564
4X-RAY DIFFRACTION4A565 - 642
5X-RAY DIFFRACTION5B241 - 316
6X-RAY DIFFRACTION6B317 - 464
7X-RAY DIFFRACTION7B465 - 587
8X-RAY DIFFRACTION8B588 - 640

+
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://pdbjlvh1.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