[English] 日本語
Yorodumi
- PDB-4up7: Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4up7
TitleCrystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate
ComponentsLYSINE--TRNA LIGASE
KeywordsLIGASE / AMINOACYLATION
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 ...Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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. / 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
ADENOSINE-5'-[LYSYL-PHOSPHATE] / Lysine--tRNA ligase
Similarity search - Component
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 Å
AuthorsBonnefond, L. / Nureki, O.
CitationJournal: FEBS Lett. / Year: 2014
Title: Crystal Structures of Entamoeba Histolytica Lysyl-tRNA Synthetase Reveal Conformational Changes Upon Lysine Binding and a Specific Helix Bundle Domain.
Authors: Bonnefond, L. / Castro De Moura, M. / Ribas De Pouplana, L. / Nureki, O.
History
DepositionJun 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Dec 10, 2014Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2172
Polymers87,7411
Non-polymers4751
Water00
1
A: LYSINE--TRNA LIGASE
hetero molecules

A: LYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,4334
Polymers175,4822
Non-polymers9512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_745-x+2,-y-1,z1
Buried area10540 Å2
ΔGint-39.1 kcal/mol
Surface area44870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.765, 155.765, 95.292
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein LYSINE--TRNA LIGASE / LYSYL-TRNA SYNTHETASE


Mass: 87741.219 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTAMOEBA HISTOLYTICA (eukaryote) / Plasmid: PET-30 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41(DE3) ROSETTA / References: UniProt: C4M7X2, lysine-tRNA ligase
#2: Chemical ChemComp-LAD / ADENOSINE-5'-[LYSYL-PHOSPHATE]


Mass: 475.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N7O8P

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.6 % / Description: NONE
Crystal growpH: 8
Details: 50 MM HEPES PH 8.0, 50 MM NACL, 1 MM SPERMINE, 8% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→37.4 Å / Num. obs: 32784 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 22.8 % / Biso Wilson estimate: 76.48 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 22.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 22.2 % / Mean I/σ(I) obs: 1.8 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BJU

3bju


Resolution: 2.789→36.047 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 1707 5.2 %
Rwork0.2053 --
obs0.2063 32754 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.2 Å2
Refinement stepCycle: LAST / Resolution: 2.789→36.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 32 0 4271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034363
X-RAY DIFFRACTIONf_angle_d0.8015895
X-RAY DIFFRACTIONf_dihedral_angle_d13.7371659
X-RAY DIFFRACTIONf_chiral_restr0.03654
X-RAY DIFFRACTIONf_plane_restr0.003759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7892-2.87130.4851160.38862441X-RAY DIFFRACTION95
2.8713-2.96390.35471390.31682611X-RAY DIFFRACTION100
2.9639-3.06980.31641440.25822577X-RAY DIFFRACTION100
3.0698-3.19260.28041380.25442597X-RAY DIFFRACTION100
3.1926-3.33780.31331360.25582578X-RAY DIFFRACTION100
3.3378-3.51370.22321530.22232601X-RAY DIFFRACTION100
3.5137-3.73360.20071310.20342586X-RAY DIFFRACTION100
3.7336-4.02150.2251490.18752598X-RAY DIFFRACTION100
4.0215-4.42560.20661660.17052566X-RAY DIFFRACTION100
4.4256-5.06450.17581590.15182596X-RAY DIFFRACTION100
5.0645-6.37490.23871620.20592599X-RAY DIFFRACTION100
6.3749-36.05050.18691140.20432697X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 181.8448 Å / Origin y: -63.8053 Å / Origin z: -15.4699 Å
111213212223313233
T0.4742 Å20.0939 Å20.0354 Å2-0.5922 Å2-0.131 Å2--0.4314 Å2
L2.9121 °21.9153 °2-0.0093 °2-1.7535 °2-0.0338 °2--0.3369 °2
S0.3055 Å °-0.6357 Å °0.6005 Å °0.3141 Å °-0.3649 Å °0.4565 Å °-0.0555 Å °-0.0471 Å °0.0952 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 2:591)

+
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