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- PDB-2x1m: Crystal structure of Mycobacterium smegmatis methionyl-tRNA synth... -

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Basic information

Entry
Database: PDB / ID: 2x1m
TitleCrystal structure of Mycobacterium smegmatis methionyl-tRNA synthetase in complex with methionine
ComponentsMETHIONYL-TRNA SYNTHETASE
KeywordsLIGASE / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / AMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP 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
DIHYDROGENPHOSPHATE ION / METHIONINE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIngvarsson, H. / Jones, T.A. / Unge, T.
Citation
Journal: FEBS J. / Year: 2010
Title: Flexibility and Communication within the Structure of the Mycobacterium Smegmatis Methionyl-tRNA Synthetase.
Authors: Ingvarsson, H. / Unge, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization of Mycobacterium Smegmatis Methionyl-tRNA Synthetase in the Presence of Methionine and Adenosine.
Authors: Ingvarsson, H. / Jones, T.A. / Unge, T.
History
DepositionDec 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6434
Polymers59,1751
Non-polymers4683
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)209.990, 209.990, 73.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein METHIONYL-TRNA SYNTHETASE


Mass: 59175.215 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: A0R3E2, methionine-tRNA ligase
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M NAH2PO4, 800 MM K2HPO4, 200 MM LI2SO4, 100 MM CAPS, PH 7.0, VAPOR DIFFUSION, HANGING DROPS, TEMPERATURE 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 23, 2009 / Details: MULTILAYER MIRROR
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 15164 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A8H

1a8h


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.77 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.85 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 756 5 %RANDOM
Rwork0.21 ---
obs0.212 14405 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å2-1.29 Å20 Å2
2---2.58 Å20 Å2
3---3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 28 16 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224210
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8111.9555730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8965510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31823.173208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17715659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3791536
X-RAY DIFFRACTIONr_chiral_restr0.0520.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0830.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 56 -
Rwork0.289 1044 -
obs--99.2 %

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