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- PDB-5gl7: Crystal structure of a truncated human cytosolic methionyl-tRNA s... -

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Basic information

Entry
Database: PDB / ID: 5gl7
TitleCrystal structure of a truncated human cytosolic methionyl-tRNA synthetase
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 / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / 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 / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / 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--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.013 Å
AuthorsCho, H.Y. / Lee, H.J. / Kang, B.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research FoundationNRF-2014M3A6A4062857 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of a truncated human cytosolic methionyl-tRNA synthetase
Authors: Cho, H.Y. / Lee, H.J. / Kang, B.S.
History
DepositionJul 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,3595
Polymers71,0441
Non-polymers3154
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-3 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.035, 93.030, 122.084
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris pH 7.5, 200mM magnesium chloride, 5mM DTT, 21% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.013→50 Å / Num. obs: 48954 / % possible obs: 98.2 % / Redundancy: 6.7 % / Net I/σ(I): 26.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1690phasing
PHENIX1.9_1690refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: zinc phazing model

Resolution: 2.013→37.284 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2256 2000 4.09 %
Rwork0.1944 --
obs0.1957 48889 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.013→37.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 14 345 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024910
X-RAY DIFFRACTIONf_angle_d0.6986676
X-RAY DIFFRACTIONf_dihedral_angle_d13.851806
X-RAY DIFFRACTIONf_chiral_restr0.028732
X-RAY DIFFRACTIONf_plane_restr0.003865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0133-2.06370.31351330.29353116X-RAY DIFFRACTION93
2.0637-2.11950.3111400.26983302X-RAY DIFFRACTION98
2.1195-2.18180.29251410.26043296X-RAY DIFFRACTION98
2.1818-2.25230.28541420.24143314X-RAY DIFFRACTION98
2.2523-2.33270.26191400.24143291X-RAY DIFFRACTION98
2.3327-2.42610.26031420.23643324X-RAY DIFFRACTION98
2.4261-2.53650.3091400.22843303X-RAY DIFFRACTION98
2.5365-2.67020.25881440.22983343X-RAY DIFFRACTION98
2.6702-2.83750.27981420.22113349X-RAY DIFFRACTION98
2.8375-3.05650.2511440.2143369X-RAY DIFFRACTION99
3.0565-3.36390.23431450.19833403X-RAY DIFFRACTION100
3.3639-3.85020.20021470.17443456X-RAY DIFFRACTION100
3.8502-4.84920.18911470.1463460X-RAY DIFFRACTION100
4.8492-37.290.16151530.15973563X-RAY DIFFRACTION98

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