[English] 日本語
Yorodumi
- PDB-7db8: Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7db8
TitleCrystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound PF-3845
Components
  • Phenylalanine--tRNA ligase alpha subunit
  • Phenylalanine--tRNA ligase beta subunit
KeywordsLIGASE / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain ...Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / 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 / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-H2R / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, M. / Zhang, X. / Xu, L. / Chen, S.
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis .
Authors: Wang, H. / Xu, M. / Engelhart, C.A. / Zhang, X. / Yan, B. / Pan, M. / Xu, Y. / Fan, S. / Liu, R. / Xu, L. / Hua, L. / Schnappinger, D. / Chen, S.
#1: Journal: J.Biol.Chem. / Year: 2021
Title: Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis
Authors: Wang, H. / Xu, M. / Engelhart, C.A. / Zhang, X. / Yan, B. / Pan, M. / Xu, Y. / Fan, S. / Liu, R. / Xu, L. / Hua, L. / Schnappinger, D. / Chen, S.
History
DepositionOct 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,30016
Polymers127,5952
Non-polymers1,70514
Water18,4831026
1
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules

A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,60132
Polymers255,1904
Non-polymers3,41128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area25050 Å2
ΔGint-169 kcal/mol
Surface area86250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.005, 297.814, 65.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 37415.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheS, Rv1649, MTCY06H11.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 90179.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheT, Rv1650, MTCY06H11.15 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU1, phenylalanine-tRNA ligase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-H2R / N-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide


Mass: 456.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23F3N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5M (NH4)2SO4, 0.2% PEG 3350, 0.1M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 121928 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 29.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.138 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 6050 / CC1/2: 0.953 / % possible all: 100

-
Processing

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

7daw


Resolution: 2.3→49.64 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1864 5476 4.89 %
Rwork0.1682 106404 -
obs0.1691 111880 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8341 0 98 1026 9465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818669
X-RAY DIFFRACTIONf_angle_d0.979611861
X-RAY DIFFRACTIONf_chiral_restr0.05961336
X-RAY DIFFRACTIONf_plane_restr0.00641594
X-RAY DIFFRACTIONf_dihedral_angle_d22.86143186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.24311430.20012617X-RAY DIFFRACTION68.25
2.33-2.350.20381200.19362712X-RAY DIFFRACTION69.6
2.35-2.380.26191360.1892684X-RAY DIFFRACTION71.14
2.38-2.410.21321260.1952814X-RAY DIFFRACTION73.56
2.41-2.440.21490.22928X-RAY DIFFRACTION75.69
2.44-2.480.23521280.19232929X-RAY DIFFRACTION77.29
2.48-2.510.22951350.20083063X-RAY DIFFRACTION78.81
2.51-2.550.22911280.20333156X-RAY DIFFRACTION81.15
2.55-2.590.24761600.23174X-RAY DIFFRACTION83.98
2.59-2.630.21831590.20793453X-RAY DIFFRACTION88.53
2.63-2.680.26522140.21643443X-RAY DIFFRACTION91.52
2.68-2.730.23112020.20773664X-RAY DIFFRACTION95.36
2.73-2.780.24011920.19923738X-RAY DIFFRACTION97.96
2.78-2.840.19912130.18913780X-RAY DIFFRACTION98.84
2.84-2.90.20631920.19623831X-RAY DIFFRACTION99.6
2.9-2.970.21641820.19013852X-RAY DIFFRACTION99.93
2.97-3.040.22092130.18643825X-RAY DIFFRACTION100
3.04-3.120.22272310.18553825X-RAY DIFFRACTION99.98
3.12-3.210.19571980.18683820X-RAY DIFFRACTION100
3.21-3.320.22391910.17613905X-RAY DIFFRACTION99.98
3.32-3.440.23491830.17163858X-RAY DIFFRACTION100
3.44-3.570.16272090.16193850X-RAY DIFFRACTION99.98
3.57-3.740.15781910.14813886X-RAY DIFFRACTION99.98
3.74-3.930.14632200.14393854X-RAY DIFFRACTION99.98
3.93-4.180.14772010.13573906X-RAY DIFFRACTION100
4.18-4.50.14512250.12643853X-RAY DIFFRACTION99.98
4.5-4.950.1422450.12833890X-RAY DIFFRACTION100
4.95-5.670.16951690.15253967X-RAY DIFFRACTION100
5.67-7.140.16812250.17113973X-RAY DIFFRACTION99.98
7.14-49.640.17081960.16624154X-RAY DIFFRACTION99.61

+
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