[English] 日本語
Yorodumi
- PDB-6sjc: Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-asp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sjc
TitleStructure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)adenosine
ComponentsAspartate--tRNA(Asp) ligase
KeywordsLIGASE / protein-inhibitor complex / tRNA aminoacylation
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Aspartate-tRNA ligase, type 1 / : / : / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type ...Aspartate-tRNA ligase, type 1 / : / : / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
5'-O-(L-alpha-aspartylsulfamoyl)adenosine / Aspartate--tRNA(Asp) ligase / Aspartate--tRNA(Asp) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders1S53518N Belgium
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Aspartate--tRNA(Asp) ligase
B: Aspartate--tRNA(Asp) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2864
Polymers132,3642
Non-polymers9232
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-58 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.089, 112.764, 88.073
Angle α, β, γ (deg.)90.000, 104.170, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Aspartate--tRNA(Asp) ligase / Aspartyl-tRNA synthetase / AspRS / Discriminating aspartyl-tRNA synthetase / D-AspRS


Mass: 66181.828 Da / Num. of mol.: 2 / Fragment: aspartyl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: aspS / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta 2 (DE3) pLysS
References: UniProt: P36419, UniProt: Q5SKD2*PLUS, aspartate-tRNA ligase
#2: Chemical ChemComp-DSZ / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine


Mass: 461.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were ...Details: A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were grown by mixing an equal volume of the protein solution with 8-12% PEG 4000, 0.1 M Morpheus buffer system 1 (MES/imidazole) pH 7, 100 mM KCl, 20 v/v % glycerol. For soaking a 4 mM solution of compound in DMSO was used. A one third volume of the initial drop size was pipetted carefully onto the crystal containing drop. The sample was then placed back over the reservoir and incubated for approximately 2 hr. Crystals were caught in cryoloops and directly flash frozen in liquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 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: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.16→79.59 Å / Num. obs: 83261 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 13.4 / Num. measured all: 583963
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
2.16-2.276.91.09583169120660.720.4481.1841.699.3
6.82-79.596.80.0341859527200.9990.0140.03741.699.7

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LOW

1low


Resolution: 2.23→57.581 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2177 2.88 %
Rwork0.1866 73339 -
obs0.188 75516 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.84 Å2 / Biso mean: 67.9309 Å2 / Biso min: 34.14 Å2
Refinement stepCycle: final / Resolution: 2.23→57.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9018 0 62 193 9273
Biso mean--56.1 57.6 -
Num. residues----1157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.23-2.27850.33681360.2805457399
2.2785-2.33150.33811450.2528453299
2.3315-2.38980.30151310.2362454699
2.3898-2.45440.29581370.2328455099
2.4544-2.52670.27161430.21884551100
2.5267-2.60820.22771330.20564572100
2.6082-2.70140.25671160.20484573100
2.7014-2.80960.27871250.21184574100
2.8096-2.93750.32161320.21544584100
2.9375-3.09230.28251220.22134597100
3.0923-3.2860.24081310.21374611100
3.286-3.53970.26431620.20524560100
3.5397-3.89590.22921410.18894611100
3.8959-4.45940.21721540.15994577100
4.4594-5.61770.18771380.15674642100
5.6177-57.5810.18691310.16244686100
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)
10.7566-0.0849-0.01270.6919-0.04910.581-0.0174-0.12630.10620.15330.1067-0.0384-0.01130.0308-0.08880.41220.00560.04570.4051-0.01350.3894-27.09926.5802-15.7351
20.8353-0.2935-0.35640.64110.23280.791-0.0135-0.034-0.13280.09360.09210.05920.1915-0.0659-0.0630.4877-0.0574-0.02050.40460.03670.4583-37.1559-20.1315-20.3088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 578 )A0 - 578
2X-RAY DIFFRACTION2chain 'B' and (not resid 300:412 )B

+
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