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- PDB-5h34: Crystal structure of the C-terminal domain of methionyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 5h34
TitleCrystal structure of the C-terminal domain of methionyl-tRNA synthetase (MetRS-C) in Nanoarchaeum equitans
ComponentsMethionine-tRNA ligaseMethionine—tRNA ligase
KeywordsLIGASE / tRNA / methionyl-tRNA synthetase / Nanoarchaeum equitans
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Methionyl-tRNA synthetase, Zn-domain / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site ...Methionyl-tRNA synthetase, Zn-domain / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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. / Nucleic acid-binding proteins / Rossmann-like alpha/beta/alpha sandwich fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Methionine--tRNA ligase
Similarity search - Component
Biological speciesNanoarchaeum equitans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.748 Å
AuthorsSuzuki, H. / Kaneko, A. / Yamamoto, T. / Nambo, M. / Umehara, T. / Yoshida, H. / Park, S.Y. / Tamura, K.
CitationJournal: J. Mol. Evol. / Year: 2017
Title: Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans.
Authors: Suzuki, H. / Kaneko, A. / Yamamoto, T. / Nambo, M. / Hirasawa, I. / Umehara, T. / Yoshida, H. / Park, S.Y. / Tamura, K.
History
DepositionOct 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Methionine-tRNA ligase
B: Methionine-tRNA ligase


Theoretical massNumber of molelcules
Total (without water)30,1412
Polymers30,1412
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-24 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.638, 58.824, 59.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15070.533 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 663-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (archaea) / Strain: Kin4-M / Gene: metG, NEQ457 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74MZ1, methionine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30%(w/v) PEG 4000, 0.2M Ammonium acetate, 0.1M Sodium acetate trihydrate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.748→41.827 Å / Num. obs: 18875 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.7
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.2 / % possible all: 91.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.748→41.827 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2368 938 5.01 %
Rwork0.1827 --
obs0.1852 18705 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.748→41.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 0 158 1909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071773
X-RAY DIFFRACTIONf_angle_d0.8862379
X-RAY DIFFRACTIONf_dihedral_angle_d16.4911107
X-RAY DIFFRACTIONf_chiral_restr0.059273
X-RAY DIFFRACTIONf_plane_restr0.005299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7485-1.84070.27321450.20232393X-RAY DIFFRACTION96
1.8407-1.9560.27621470.1942504X-RAY DIFFRACTION100
1.956-2.1070.24481130.18382535X-RAY DIFFRACTION100
2.107-2.3190.22251420.18552546X-RAY DIFFRACTION100
2.319-2.65450.24031320.19762549X-RAY DIFFRACTION100
2.6545-3.34420.24331440.18662542X-RAY DIFFRACTION99
3.3442-41.83920.21881150.16952698X-RAY DIFFRACTION98

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