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- PDB-5xgq: Crystal structure of apo form (free-state) Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 5xgq
TitleCrystal structure of apo form (free-state) Mycobacterium tuberculosis methionyl-tRNA synthetase
ComponentsMethionine-tRNA ligase
KeywordsLIGASE / Methionyl-tRNA Synthetase / Protein translation / Mycobacterium tuberculosis / Anticodon-binding domain of tRNA
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
Methionine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsWang, W. / Wang, M. / Wojdyla, J.A. / 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 15, 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.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _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
B: Methionine-tRNA ligase
A: Methionine-tRNA ligase


Theoretical massNumber of molelcules
Total (without water)120,4972
Polymers120,4972
Non-polymers00
Water20,9511163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area45660 Å2
Unit cell
Length a, b, c (Å)49.983, 72.727, 78.376
Angle α, β, γ (deg.)98.90, 90.05, 98.47
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 60248.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: metG, MRA_1016 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)pLysS AG / References: UniProt: A5U150, methionine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / 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: 2.31 Å3/Da / Density % sol: 46.75 % / Description: plates
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.1
Details: 0.1M calcium acetate, 0.1M sodium cacodylate, 16%PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: AREA DETECTOR / Date: Aug 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.899→48.686 Å / Num. obs: 158725 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 1.68 % / Biso Wilson estimate: 28.233 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Χ2: 0.97 / Net I/σ(I): 6.68
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 1.53 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 27608 / CC1/2: 0.586 / Χ2: 0.88

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Processing

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

2x1l


Resolution: 1.899→48.686 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 7918 4.99 %Random
Rwork0.2018 ---
obs0.2035 158552 93.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→48.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 0 1163 9079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038134
X-RAY DIFFRACTIONf_angle_d0.58911083
X-RAY DIFFRACTIONf_dihedral_angle_d13.9824779
X-RAY DIFFRACTIONf_chiral_restr0.041200
X-RAY DIFFRACTIONf_plane_restr0.0041453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8994-1.9210.47742210.40694236X-RAY DIFFRACTION77
1.921-1.94360.33452600.3484935X-RAY DIFFRACTION94
1.9436-1.96730.32242720.31255051X-RAY DIFFRACTION93
1.9673-1.99220.34772670.29835069X-RAY DIFFRACTION94
1.9922-2.01840.29422740.27295163X-RAY DIFFRACTION95
2.0184-2.04610.2862620.27984963X-RAY DIFFRACTION93
2.0461-2.07530.34542510.29344752X-RAY DIFFRACTION88
2.0753-2.10630.32272650.27664981X-RAY DIFFRACTION93
2.1063-2.13920.29642640.24785086X-RAY DIFFRACTION94
2.1392-2.17430.28512770.2475121X-RAY DIFFRACTION94
2.1743-2.21180.26272660.23845020X-RAY DIFFRACTION94
2.2118-2.2520.29582540.24684878X-RAY DIFFRACTION90
2.252-2.29530.27632650.23535013X-RAY DIFFRACTION93
2.2953-2.34220.28322690.22535141X-RAY DIFFRACTION94
2.3422-2.39310.2572680.21475095X-RAY DIFFRACTION95
2.3931-2.44880.25132730.20775175X-RAY DIFFRACTION95
2.4488-2.510.27182660.21035088X-RAY DIFFRACTION95
2.51-2.57780.25582660.2065102X-RAY DIFFRACTION95
2.5778-2.65370.25452650.21155191X-RAY DIFFRACTION95
2.6537-2.73930.26342660.20145057X-RAY DIFFRACTION94
2.7393-2.83720.22152620.18745054X-RAY DIFFRACTION95
2.8372-2.95080.22892760.18325194X-RAY DIFFRACTION95
2.9508-3.08510.22492660.19175098X-RAY DIFFRACTION95
3.0851-3.24770.22472670.18135100X-RAY DIFFRACTION95
3.2477-3.45120.18422610.17144994X-RAY DIFFRACTION92
3.4512-3.71750.20272610.15924928X-RAY DIFFRACTION92
3.7175-4.09150.16992580.15974993X-RAY DIFFRACTION92
4.0915-4.68310.20182630.14354968X-RAY DIFFRACTION94
4.6831-5.89860.20162670.17095083X-RAY DIFFRACTION94
5.8986-48.70170.17672660.18735105X-RAY DIFFRACTION94

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