[English] 日本語
Yorodumi
- PDB-8wih: Crystal structure of E. coli ThrS catalytic domain mutant G463A i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wih
TitleCrystal structure of E. coli ThrS catalytic domain mutant G463A in complex with ATP
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
Function / homologyADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsQiao, H. / Wang, Z. / Wang, J. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977107, 22277132 China
CitationJournal: Commun Biol / Year: 2024
Title: Specific glycine-dependent enzyme motion determines the potency of conformation selective inhibitors of threonyl-tRNA synthetase.
Authors: Qiao, H. / Wang, Z. / Yang, H. / Xia, M. / Yang, G. / Bai, F. / Wang, J. / Fang, P.
History
DepositionSep 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Threonine--tRNA ligase
B: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0286
Polymers95,8832
Non-polymers1,1454
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-94 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.175, 109.376, 113.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 47941.543 Da / Num. of mol.: 2 / Mutation: G463A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thrS, CX696_002870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8S7FUD7, threonine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 0.045 M imidazole, 0.055 M MES monohydrate acid pH 6.5, 20% v/v glycerol, 10% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.44→78.86 Å / Num. obs: 36771 / % possible obs: 88.7 % / Redundancy: 8.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Rrim(I) all: 0.12 / Χ2: 0.97 / Net I/σ(I): 14.2 / Num. measured all: 325461
Reflection shellResolution: 2.44→2.57 Å / % possible obs: 98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.814 / Num. measured all: 38067 / Num. unique obs: 5811 / CC1/2: 0.838 / Rpim(I) all: 0.334 / Rrim(I) all: 0.885 / Χ2: 0.83 / Net I/σ(I) obs: 2.7

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→50.48 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1850 5.04 %
Rwork0.2402 --
obs0.2414 36684 88.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 52 48 6498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036594
X-RAY DIFFRACTIONf_angle_d0.5578912
X-RAY DIFFRACTIONf_dihedral_angle_d5.696890
X-RAY DIFFRACTIONf_chiral_restr0.042949
X-RAY DIFFRACTIONf_plane_restr0.0051152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.520.37392340.3333693X-RAY DIFFRACTION97
2.52-2.620.34631920.32263868X-RAY DIFFRACTION99
2.62-2.740.28011370.3132430X-RAY DIFFRACTION62
2.74-2.890.31151930.29823857X-RAY DIFFRACTION100
2.89-3.070.3142090.29453899X-RAY DIFFRACTION100
3.07-3.30.29952050.27333908X-RAY DIFFRACTION100
3.3-3.620.28041290.24752673X-RAY DIFFRACTION71
3.7-4.160.24471260.21252395X-RAY DIFFRACTION72
4.16-5.240.1872040.17663993X-RAY DIFFRACTION100
5.25-50.480.25612210.22114118X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -23.8041 Å / Origin y: 22.0468 Å / Origin z: -24.0931 Å
111213212223313233
T0.2711 Å20.0097 Å2-0.0036 Å2-0.2914 Å20.0013 Å2--0.2759 Å2
L0.7665 °20.064 °20.1595 °2-0.7931 °2-0.1056 °2--0.6009 °2
S0.0206 Å °-0.0317 Å °0.0183 Å °-0.0539 Å °-0.0527 Å °0.0436 Å °0.013 Å °-0.0273 Å °0.0357 Å °
Refinement TLS groupSelection details: all

+
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