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- PDB-1pfv: METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH DI... -

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Basic information

Entry
Database: PDB / ID: 1pfv
TitleMETHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH DIFLUOROMETHIONINE
ComponentsMethionyl-tRNA synthetase
KeywordsLIGASE / Rossmann fold
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
Methionyl-tRNA synthetase, Zn-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 ...Methionyl-tRNA synthetase, Zn-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 / Rubrerythrin, domain 2 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Single Sheet / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-(DIFLUOROMETHYL)HOMOCYSTEINE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)63,2093
Polymers62,9581
Non-polymers2512
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.573, 45.221, 86.068
Angle α, β, γ (deg.)90.00, 107.37, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2FM / S-(DIFLUOROMETHYL)HOMOCYSTEINE / DIFLUOROMETHIONINE


Type: L-peptide linking / Mass: 185.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9F2NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
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: Feb 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→74 Å / Num. all: 63519 / Num. obs: 63519 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 4755 / Rsym value: 0.19 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 63973 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.19

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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: 1.7→74 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3197 -random
Rwork0.186 ---
obs0.186 63519 99.2 %-
all-63999 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.116 Å20 Å2-0.174 Å2
2---0.222 Å20 Å2
3---0.107 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 12 541 4943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.19
X-RAY DIFFRACTIONc_bond_d0.0048
LS refinement shellResolution: 1.7→1.71 Å
RfactorNum. reflection
Rfree0.291 66
Rwork0.253 -
obs-1292
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.18

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