[English] 日本語
Yorodumi
- PDB-9drs: Crystal structure of M. tuberculosis PheRS-tRNA complex bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9drs
TitleCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(Phe)
KeywordsLIGASE/RNA / RNA ligase aminoacyl-tRNA synthetase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / RNA BINDING PROTEIN / LIGASE-RNA complex
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / B3/4 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 / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / 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 / 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, OB-fold
Similarity search - Domain/homology
ACETATE ION / 1H-benzimidazol-2-amine / DI(HYDROXYETHYL)ETHER / : / RNA / RNA (> 10) / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGade, P. / Chang, C. / Forte, B. / Wower, J. / Gilbert, I.H. / Baragana, B. / Michalska, K. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase.
Authors: Gade, P. / Chang, C. / Pryde, D.S. / Fletcher, D. / Niven, S. / Magalhaes, L.G. / Robinson, D. / Saini, J. / Ibrahim, P.E.G.F. / Forte, B. / Wower, J. / Bodkin, M.J. / Baragana, B. / ...Authors: Gade, P. / Chang, C. / Pryde, D.S. / Fletcher, D. / Niven, S. / Magalhaes, L.G. / Robinson, D. / Saini, J. / Ibrahim, P.E.G.F. / Forte, B. / Wower, J. / Bodkin, M.J. / Baragana, B. / Gilbert, I.H. / Michalska, K. / Joachimiak, A.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
D: Phenylalanine--tRNA ligase alpha subunit
E: Phenylalanine--tRNA ligase beta subunit
F: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,86945
Polymers302,2516
Non-polymers2,61939
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40190 Å2
ΔGint-207 kcal/mol
Surface area108730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.676, 64.106, 188.334
Angle α, β, γ (deg.)90.00, 111.21, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Phenylalanine--tRNA ligase ... , 2 types, 4 molecules ADBE

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


Mass: 37415.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pheS, Rv1649, MTCY06H11.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 88867.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pheT, Rv1650, MTCY06H11.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU1, phenylalanine-tRNA ligase

-
RNA chain , 1 types, 2 molecules CF

#3: RNA chain tRNA(Phe)


Mass: 24842.811 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
References: GenBank: 1251771558

-
Non-polymers , 8 types, 761 molecules

#4: Chemical ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Acetate, 0.1 M Hepes pH 7.5, 25 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 135377 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 16.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6682 / CC1/2: 0.549 / CC star: 0.842 / Rpim(I) all: 0.486 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.77 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 10245 5.04 %
Rwork0.2006 --
obs0.2031 127062 76.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17318 3045 170 722 21255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221258
X-RAY DIFFRACTIONf_angle_d0.4529676
X-RAY DIFFRACTIONf_dihedral_angle_d9.3844258
X-RAY DIFFRACTIONf_chiral_restr0.0383510
X-RAY DIFFRACTIONf_plane_restr0.0043399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.38591060.32872176X-RAY DIFFRACTION26
2.38-2.410.3991410.31112609X-RAY DIFFRACTION32
2.41-2.440.31951720.30353152X-RAY DIFFRACTION38
2.44-2.470.32191880.29713701X-RAY DIFFRACTION43
2.47-2.50.32562450.28814056X-RAY DIFFRACTION49
2.5-2.540.31422150.27184368X-RAY DIFFRACTION52
2.54-2.570.31662660.26224709X-RAY DIFFRACTION56
2.57-2.610.2952540.24694783X-RAY DIFFRACTION58
2.61-2.650.28362830.25155039X-RAY DIFFRACTION59
2.65-2.70.28482680.25175317X-RAY DIFFRACTION64
2.7-2.740.28672680.2495681X-RAY DIFFRACTION68
2.74-2.790.29453370.25376009X-RAY DIFFRACTION71
2.79-2.850.29053360.24466365X-RAY DIFFRACTION76
2.85-2.90.31333350.24216675X-RAY DIFFRACTION79
2.9-2.970.29343960.23296867X-RAY DIFFRACTION83
2.97-3.040.29344350.22387181X-RAY DIFFRACTION86
3.04-3.110.25084030.21517455X-RAY DIFFRACTION90
3.11-3.20.2824770.20637766X-RAY DIFFRACTION92
3.2-3.290.25193930.20857608X-RAY DIFFRACTION92
3.29-3.40.25154250.20628302X-RAY DIFFRACTION98
3.4-3.520.23454390.20238241X-RAY DIFFRACTION99
3.52-3.660.25124400.18828321X-RAY DIFFRACTION99
3.66-3.820.20954430.17818360X-RAY DIFFRACTION99
3.82-4.030.22944650.17928336X-RAY DIFFRACTION99
4.03-4.280.21934360.17078238X-RAY DIFFRACTION98
4.28-4.610.22233720.16278402X-RAY DIFFRACTION99
4.61-5.070.21653960.16778386X-RAY DIFFRACTION100
5.07-5.80.22934570.18518367X-RAY DIFFRACTION100
5.8-7.310.23054310.19288248X-RAY DIFFRACTION99
7.31-46.770.22434230.17438306X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.1972 Å / Origin y: 0.0412 Å / Origin z: 45.0665 Å
111213212223313233
T0.1079 Å2-0.032 Å2-0.0073 Å2-0.0761 Å2-0.0167 Å2--0.1117 Å2
L0.0855 °2-0.0472 °2-0.1074 °2-0.0259 °20.0075 °2--0.2256 °2
S-0.013 Å °0.0723 Å °-0.0184 Å °0.0054 Å °0.0048 Å °0.0118 Å °0.0517 Å °-0.0403 Å °-0.0027 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