[English] 日本語
Yorodumi
- PDB-1il2: Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1il2
TitleCrystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex
Components
  • ASPARTYL TRANSFER RNA
  • ASPARTYL-TRNA SYNTHETASE
KeywordsLIGASE/RNA / protein-rna complex / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytosol
Similarity search - Function
GAD-like domain / 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) ...GAD-like domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Gyrase A; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE / : / RNA / RNA (> 10) / Aspartate--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMoulinier, L. / Eiler, S. / Eriani, G. / Gangloff, J. / Thierry, J.C. / Gabriel, K. / McClain, W.H. / Moras, D.
CitationJournal: EMBO J. / Year: 2001
Title: The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.
Authors: Moulinier, L. / Eiler, S. / Eriani, G. / Gangloff, J. / Thierry, J.C. / Gabriel, K. / McClain, W.H. / Moras, D.
History
DepositionMay 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: ASPARTYL TRANSFER RNA
D: ASPARTYL TRANSFER RNA
A: ASPARTYL-TRNA SYNTHETASE
B: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4728
Polymers180,3554
Non-polymers1,1174
Water7,242402
1
C: ASPARTYL TRANSFER RNA
A: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7364
Polymers90,1782
Non-polymers5582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: ASPARTYL TRANSFER RNA
B: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7364
Polymers90,1782
Non-polymers5582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.800, 222.800, 80.800
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: RNA chain ASPARTYL TRANSFER RNA


Mass: 24181.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176417
#2: Protein ASPARTYL-TRNA SYNTHETASE


Mass: 65996.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pbr322 / Production host: Escherichia coli (E. coli) / References: UniProt: P21889, aspartate-tRNA ligase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMO / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE


Mass: 462.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N6O10P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Components of the solutionsName: ammonium sulfate
Crystal grow
*PLUS
Details: Boeglin, M., (1996) Acta Crystallogr, D52, 211.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlAspRS1drop
21 mg/mltRNA1drop
31 mM1dropMgCl2
41.5 Mammonium sulfate1drop
575 mMBis-Tris-propane1drop
60.5 mMAMP-PCP1drop
71 mML-aspartic acid1drop
81.9 Mammonium sulfate1reservoir
9100 mMBis-Tris-propane1reservoir
101-3 %(v/v)2-propanol1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→11.5 Å / Redundancy: 2.3 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 3.7
Reflection
*PLUS
Num. obs: 72094 / % possible obs: 92 % / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 80 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.216

-
Processing

Software
NameVersionClassification
ALMNmodel building
TSFGENmodel building
CNS1refinement
CCP4(ALMNphasing
TSFGEN)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. thermophilus AspRS

Resolution: 2.6→11.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1600037.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3084 4.9 %RANDOM
Rwork0.204 ---
obs0.204 63304 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.14 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å20 Å24.7 Å2
2---7.6 Å20 Å2
3---2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→11.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 3097 72 402 12753
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.211.5
X-RAY DIFFRACTIONc_mcangle_it4.82
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.32.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 364 4.6 %
Rwork0.318 7483 -
obs--63 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TRNA.PARAMTRNA.TOP
X-RAY DIFFRACTION3LIGAND.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMLIGAND.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.318

+
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