[English] 日本語
Yorodumi
- PDB-7ent: Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ent
TitleCrystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Y-13 and ATP
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / TrpRS / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / 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. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-J9L / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, M. / Chen, S.
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents.
Authors: Yang, Y. / Xu, Y. / Yue, Y. / Wang, H. / Cui, Y. / Pan, M. / Zhang, X. / Zhang, L. / Li, H. / Xu, M. / Tang, Y. / Chen, S.
History
DepositionApr 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1844
Polymers37,3811
Non-polymers8033
Water1,27971
1
A: Tryptophan--tRNA ligase
hetero molecules

A: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3688
Polymers74,7622
Non-polymers1,6066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area6010 Å2
ΔGint-57 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.460, 61.460, 334.599
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

-
Components

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


Mass: 37380.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: trpS, DSI38_02915, E5M05_20150, E5M52_19725, E5M78_19780, ERS007657_01660, ERS007661_00440, ERS007663_02313, ERS007665_01484, ERS007670_03000, ERS007679_02115, ERS007681_00969, ERS007688_01638, ...Gene: trpS, DSI38_02915, E5M05_20150, E5M52_19725, E5M78_19780, ERS007657_01660, ERS007661_00440, ERS007663_02313, ERS007665_01484, ERS007670_03000, ERS007679_02115, ERS007681_00969, ERS007688_01638, ERS007703_02455, ERS007722_03290, ERS007741_01346, ERS013471_03442, ERS023446_03614, ERS024276_00235, ERS027659_00823, ERS094182_03915, F6W99_01991, GCL30_20825, SAMEA2683035_03669
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IZS3, tryptophan-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-J9L / (5S)-2-(methylamino)-5-[(1R)-1-(4-methyl-1H-indol-3-yl)ethyl]-1,3-oxazol-4-one


Mass: 271.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 0.2M MgCl2, 35% PEG 400, 0.1M MES, pH 5.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15814 / % possible obs: 99.7 % / Redundancy: 17.8 % / Biso Wilson estimate: 35.55 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.172 / Net I/σ(I): 19.67
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 762 / CC1/2: 0.789 / CC star: 0.939 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EL8

7el8


Resolution: 2.4→48.04 Å / SU ML: 0.2429 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 719 5.11 %
Rwork0.1953 13343 -
obs0.1982 14062 89.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 52 71 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982592
X-RAY DIFFRACTIONf_angle_d1.19643541
X-RAY DIFFRACTIONf_chiral_restr0.0602412
X-RAY DIFFRACTIONf_plane_restr0.0061478
X-RAY DIFFRACTIONf_dihedral_angle_d15.769950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.3407860.22181490X-RAY DIFFRACTION51.84
2.59-2.850.26631490.22242703X-RAY DIFFRACTION93.51
2.85-3.260.27861470.2262946X-RAY DIFFRACTION99.97
3.26-4.110.29791550.18742994X-RAY DIFFRACTION99.68
4.11-48.040.20211820.1773210X-RAY DIFFRACTION99.91

+
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