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- PDB-5goy: The crystal structure of human cytosolic methionyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 5goy
TitleThe crystal structure of human cytosolic methionyl-tRNA synthetase in complex with methionine
ComponentsMethionine--tRNA ligase, cytoplasmic
KeywordsLIGASE / MSC / MetRS
Function / homology
Function and homology information


Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / cellular response to platelet-derived growth factor stimulus / rRNA transcription ...Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / cellular response to platelet-derived growth factor stimulus / rRNA transcription / cellular response to epidermal growth factor stimulus / tRNA binding / nucleolus / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon binding domain of methionyl tRNA ligase ...Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / S15/NS1, RNA-binding
Similarity search - Domain/homology
METHIONINE / Methionine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.278 Å
AuthorsLee, H.J. / Cho, H.Y. / Kang, B.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2015R1A4A1042271 Korea, Republic Of
CitationJournal: To be published
Title: The crystal structure of human cytosolic methionyl-tRNA synthetase in complex with methionine
Authors: Lee, H.J. / Cho, H.Y. / Kang, B.S.
History
DepositionJul 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Methionine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3244
Polymers71,0441
Non-polymers2803
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-2 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.539, 93.133, 122.482
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, cytoplasmic / Methionyl-tRNA synthetase / MetRS


Mass: 71043.781 Da / Num. of mol.: 1 / Fragment: UNP residues 221-834
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56192, methionine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.63 Å3/Da / Density meas: 53.24 Mg/m3 / Density % sol: 53.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris pH8.0, 200 mM magnesium chloride, 100 mM potassium sodium tartrate tetrahydrate, 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.278→50 Å / Num. obs: 33132 / % possible obs: 95.3 % / Redundancy: 6.7 % / Net I/σ(I): 24.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
PHENIX1.9_1690refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GL7

5gl7


Resolution: 2.278→30.699 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.2416 1999 6.04 %
Rwork0.1964 --
obs0.1991 33071 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.278→30.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4779 0 11 232 5022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034907
X-RAY DIFFRACTIONf_angle_d0.726673
X-RAY DIFFRACTIONf_dihedral_angle_d14.2031802
X-RAY DIFFRACTIONf_chiral_restr0.027733
X-RAY DIFFRACTIONf_plane_restr0.004866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2782-2.33520.3584990.29991549X-RAY DIFFRACTION67
2.3352-2.39830.36511400.28172173X-RAY DIFFRACTION94
2.3983-2.46880.30211440.25952229X-RAY DIFFRACTION96
2.4688-2.54850.30891410.25462210X-RAY DIFFRACTION96
2.5485-2.63950.34551450.2562239X-RAY DIFFRACTION96
2.6395-2.74510.27661420.2432210X-RAY DIFFRACTION95
2.7451-2.870.28571430.23822222X-RAY DIFFRACTION96
2.87-3.02120.30621440.23342230X-RAY DIFFRACTION95
3.0212-3.21030.27711430.22212240X-RAY DIFFRACTION96
3.2103-3.45780.27531460.20532254X-RAY DIFFRACTION96
3.4578-3.80520.23641490.17822321X-RAY DIFFRACTION99
3.8052-4.35450.20111510.15932359X-RAY DIFFRACTION99
4.3545-5.48110.17851530.14882388X-RAY DIFFRACTION100
5.4811-30.70180.17421590.16222448X-RAY DIFFRACTION98

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