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- PDB-1pg0: Methionyl-trna synthetase from escherichia coli complexed with me... -

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Basic information

Entry
Database: PDB / ID: 1pg0
TitleMethionyl-trna synthetase from escherichia coli complexed with methioninyl adenylate
ComponentsMethionyl-tRNA synthetase
KeywordsLIGASE / Rossmann fold
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / 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 / tRNA-binding domain ...Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / 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 / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
L-METHIONYL ADENYLATE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCrepin, T. / Schmitt, E. / Mechulam, Y. / Sampson, P.B. / Vaughan, M.D. / Honek, J.F. / Blanquet, S.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.
Authors: Crepin, T. / Schmitt, E. / Mechulam, Y. / Sampson, P.B. / Vaughan, M.D. / Honek, J.F. / Blanquet, S.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4252
Polymers62,9581
Non-polymers4661
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.041, 45.574, 87.280
Angle α, β, γ (deg.)90.00, 108.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 62958.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metG / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): JM101Tr / References: UniProt: P00959, methionine-tRNA ligase
#2: Chemical ChemComp-MOD / L-METHIONYL ADENYLATE


Type: L-peptide linking / Mass: 466.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27N6O7PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 7
Details: AMMONIUM CITRATE, POTASSIUM PHOSPHATE, pH 7, VAPOR DIFFUSION, temperature 280K
Crystal grow
*PLUS
Method: unknown / Details: Mechulam, Y., (1999) J. Mol. Biol., 294, 1287.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→33 Å / Num. all: 45389 / Num. obs: 45389 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.093 / Net I/σ(I): 4.4
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 6740 / Rsym value: 0.289 / % possible all: 93
Reflection
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.289

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQT

1qqt


Resolution: 1.9→33 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2229 -random
Rwork0.223 ---
obs0.223 44242 95.4 %-
all-44242 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.462 Å20 Å22.294 Å2
2--4.333 Å20 Å2
3---3.129 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 30 349 4360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_bond_d0.0058
LS refinement shellResolution: 1.9→1.91 Å /
RfactorNum. reflection
Rfree0.395 34
Rwork0.335 -
obs-885
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0056

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