[English] 日本語
Yorodumi
- PDB-6ykv: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ykv
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11g
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / Rossmann fold / tRNA synthetase
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-OVQ / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsPang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G077814N Belgium
Research Foundation - Flanders (FWO)G0A4616A Belgium
Research Foundation - Flanders (FWO)1109117N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors.
Authors: De Ruysscher, D. / Pang, L. / Lenders, S.M.G. / Cappoen, D. / Cos, P. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9887
Polymers98,1851
Non-polymers8036
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint7 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.109, 80.729, 224.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 98185.344 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: D454N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: leuS, VT05_02036, WHOO_00006, WHOO_00455 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS
References: UniProt: A0A5K1KQ39, UniProt: Q5FAJ3*PLUS, leucine-tRNA ligase

-
Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-OVQ / [(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-(4-pyridin-3-yl-1,2,3-triazol-1-yl)propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 526.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34N6O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.69 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0. ...Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0.75:1.0:0.25 (v/v) ratio. The seed stock was prepared in the same crystallization buffer. Suitable crystals were soaked with 2 mM synthesized compound 11g in an equilvalent precipitant solution supplemented with 22% v/v ethylene glycol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978566 Å / Relative weight: 1
ReflectionResolution: 2.36→112.19 Å / Num. obs: 37908 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.04 / Rrim(I) all: 0.129 / Net I/σ(I): 11.7 / Num. measured all: 379192
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.36-2.489.91.245401054370.6710.4081.3071.9100
7.45-112.198.90.0451218813690.9990.0150.04834.499.8

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 2.43→56.094 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 1731 5 %
Rwork0.1899 32876 -
obs0.1925 34607 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.28 Å2 / Biso mean: 58.7061 Å2 / Biso min: 25.78 Å2
Refinement stepCycle: final / Resolution: 2.43→56.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6515 0 50 136 6701
Biso mean--54.2 52.87 -
Num. residues----844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.43-2.50160.34111390.25942668
2.5016-2.58230.30661520.23692695
2.5823-2.67460.3111550.22862661
2.6746-2.78170.2891290.22052732
2.7817-2.90830.29021450.21852702
2.9083-3.06160.2871410.21462719
3.0616-3.25340.3021420.20532730
3.2534-3.50450.26841460.19512736
3.5045-3.85710.24761440.17522716
3.8571-4.41510.17981440.15952764
4.4151-5.56180.21621490.17512800
5.5618-56.0940.21241450.18512953
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)
11.29130.92740.62970.85680.45970.71910.08540.056-0.23680.14380.0484-0.21220.21940.1714-0.14570.43320.0864-0.05690.4528-0.03990.43661.6171-9.18-36.4333
20.066-0.22220.03820.8231-0.24283.69020.0288-0.1054-0.00930.00720.0380.06620.1272-0.0385-0.08250.42580.0514-0.03430.5278-0.02910.43744.77914.767-18.0695
30.85911.66870.25757.07914.57534.40120.229-0.06080.04690.2923-0.1675-0.0189-0.21220.0983-0.06820.35920.0542-0.06070.41130.03030.4415-5.821331.7873-23.6786
41.4835-0.3493-0.45290.9210.05741.71820.12670.0283-0.02580.002-0.0340.1918-0.2225-0.008-0.0880.5586-0.0072-0.02920.4066-0.00110.5285-12.701634.4002-16.7697
53.05171.68990.67463.9849-0.35992.79690.15710.0250.0550.24090.0109-0.04410.18640.4091-0.1470.4270.0568-0.08480.4932-0.06810.414321.91284.9751-20.6176
62.08550.9931.2411.34120.53252.0319-0.0086-0.0228-0.00660.02710.082-0.00550.16080.2076-0.07550.33570.0306-0.0140.3446-0.00390.32648.07786.6332-35.8028
73.18661.142-0.61611.9821-0.29150.92540.4231-0.7217-0.12260.528-0.19130.27530.09170.2262-0.2210.5699-0.0149-0.04310.4545-0.04350.4543-13.8783-6.8842-22.1426
81.8254-0.32280.9981.83581.39444.03920.1462-0.2285-0.21030.4545-0.00420.14260.5084-0.2611-0.14360.4692-0.02250.03490.36620.04060.3871-18.8092-18.0245-30.6904
95.20661.63282.12372.62540.50563.932-0.0536-0.02490.2413-0.1910.05420.3411-0.1638-0.23070.01030.28870.0454-0.01960.3075-0.02670.3344-26.0379-16.1912-54.7785
104.1158-1.14272.24211.7358-0.27122.24120.01720.52460.0964-0.0378-0.09950.4981-0.2857-0.3591-0.0360.46140.0997-0.05480.8210.00770.6573-33.5658-11.8105-62.1128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 145 )A1 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 208 )A146 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 256 )A209 - 256
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 437 )A257 - 437
5X-RAY DIFFRACTION5chain 'A' and (resid 438 through 489 )A438 - 489
6X-RAY DIFFRACTION6chain 'A' and (resid 490 through 565 )A490 - 565
7X-RAY DIFFRACTION7chain 'A' and (resid 566 through 620 )A566 - 620
8X-RAY DIFFRACTION8chain 'A' and (resid 621 through 698 )A621 - 698
9X-RAY DIFFRACTION9chain 'A' and (resid 699 through 780 )A699 - 780
10X-RAY DIFFRACTION10chain 'A' and (resid 781 through 876 )A781 - 876

+
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