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- PDB-1p7p: Methionyl-tRNA synthetase from Escherichia coli complexed with me... -

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Basic information

Entry
Database: PDB / ID: 1p7p
TitleMethionyl-tRNA synthetase from Escherichia coli complexed with methionine phosphonate
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
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
(1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHONIC ACID / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 5, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.360, 45.000, 85.950
Angle α, β, γ (deg.)90.00, 107.46, 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 4-548
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-MPH / (1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHONIC ACID / METHIONINE PHOSPHONATE


Type: L-peptide linking / Mass: 185.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
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: LURE / Beamline: DW32 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. all: 51316 / Num. obs: 51316 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 16.35 Å2 / Rsym value: 0.059
Reflection shellResolution: 1.78→1.87 Å / Redundancy: 2.1 % / Num. unique all: 7523 / Rsym value: 0.28 / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 52574 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 93.4 % / Rmerge(I) obs: 0.28

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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: 1.8→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2600 -random
Rwork0.195 ---
all0.195 53445 --
obs0.195 51316 96 %-
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 11 483 4870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.8→1.81 Å /
RfactorNum. reflection
Rfree0.232 46
Rwork0.235 -
obs-987
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.005

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