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- PDB-5xet: Crystal structure of Mycobacterium tuberculosis methionyl-tRNA sy... -

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Basic information

Entry
Database: PDB / ID: 5xet
TitleCrystal structure of Mycobacterium tuberculosis methionyl-tRNA synthetase bound by methionyl-adenylate (Met-AMP)
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / synthetase / aminoacyl-tRNA synthetase / complex / ATP
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase ...Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ME8 / Methionine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsWang, W. / Qin, B. / Wojdyla, J.A. / Wang, M. / Gao, X. / Cui, S.
CitationJournal: IUCrJ / Year: 2018
Title: Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism.
Authors: Wang, W. / Qin, B. / Wojdyla, J.A. / Wang, M. / Gao, X. / Cui, S.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0828
Polymers59,4201
Non-polymers6627
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-36 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.017, 198.017, 39.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 59419.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: metG, MRA_1016
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A5U150, methionine-tRNA ligase
#2: Chemical ChemComp-ME8 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate / L-methionine-AMP / methionyl-adenylate


Mass: 478.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H23N6O8PS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.9
Details: 0.2M Lithium sulfate monohydrate, 19% PEG 3350, bis tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.38→37.42 Å / Num. obs: 49191 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 45.55 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.156 / Net I/σ(I): 4.77
Reflection shellResolution: 2.38→2.54 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 8103 / CC1/2: 0.68 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Coot0.8.6model building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x1l

2x1l


Resolution: 2.38→37.42 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.08
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2511 1164 5.09 %
Rwork0.2009 --
obs0.2035 22866 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 40 180 4215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084134
X-RAY DIFFRACTIONf_angle_d0.8045631
X-RAY DIFFRACTIONf_dihedral_angle_d13.4562422
X-RAY DIFFRACTIONf_chiral_restr0.044616
X-RAY DIFFRACTIONf_plane_restr0.005733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.48830.31391600.27382709X-RAY DIFFRACTION100
2.4883-2.61950.34331210.2632776X-RAY DIFFRACTION100
2.6195-2.78350.26991580.2462698X-RAY DIFFRACTION100
2.7835-2.99840.2991510.23552716X-RAY DIFFRACTION100
2.9984-3.30.27751490.22282701X-RAY DIFFRACTION100
3.3-3.77710.30451290.1942709X-RAY DIFFRACTION99
3.7771-4.75720.18531360.15612710X-RAY DIFFRACTION99
4.7572-37.42630.19961600.16942683X-RAY DIFFRACTION99

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