[English] 日本語
Yorodumi
- PDB-1o5t: Crystal structure of the aminoacylation catalytic fragment of hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o5t
TitleCrystal structure of the aminoacylation catalytic fragment of human tryptophanyl-tRNA synthetase
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Rossmann fold / four helix bundle
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) ...WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S15/NS1, RNA-binding / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsYu, Y. / Liu, Y. / Shen, N. / Xu, X. / Jia, J. / Jin, Y. / Arnold, E. / Ding, J.
CitationJournal: J.BIOL.CHEM. / Year: 2004
Title: Crystal Structure of Human Tryptophanyl-tRNA Synthetase Catalytic Fragment
Authors: Yu, Y. / Liu, Y. / Shen, N. / Xu, X. / Xu, F. / Jia, J. / Jin, Y. / Arnold, E. / Ding, J.
History
DepositionOct 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)43,3861
Polymers43,3861
Non-polymers00
Water1,928107
1
A: Tryptophanyl-tRNA synthetase

A: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)86,7732
Polymers86,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_543x,x-y-1,-z-7/61
Buried area3030 Å2
ΔGint-22 kcal/mol
Surface area31460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.240, 82.240, 263.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe enzyme forms a homodimer in both solution and crystal structure. The two subunits of the dimer are related by the crystallographic 2-fold axis. Therefore, there is one molecule per asymmetric unit.

-
Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS / IFP53 / hWRS


Mass: 43386.477 Da / Num. of mol.: 1 / Fragment: aminoacylation catalytic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-Plus / References: UniProt: P23381, tryptophan-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.91 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 16% PEG1500, 4% PEG3350, 0.2M tri-sodium citrate dihydrate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916, 0.9500, 0.9790, 0.9787
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2003 / Details: mirror
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9161
20.951
30.9791
40.97871
ReflectionResolution: 2.5→30 Å / Num. all: 19164 / Num. obs: 18911 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2 / Num. unique all: 881 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.51 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2193404.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 960 5.1 %RANDOM
Rwork0.245 ---
obs0.245 18911 99 %-
all-19164 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1418 Å2 / ksol: 0.321367 e/Å3
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1-7.1 Å29.78 Å20 Å2
2--7.1 Å20 Å2
3----14.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 107 3163
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
2.5-2.660.40431534.60.34917402989
2.66-2.860.36891480.32383089
2.86-3.150.33981520.30123134
3.15-3.610.30951540.28633151
3.61-4.540.30111740.22753213
4.54-29.510.24731790.19313335
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

+
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