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Yorodumi- PDB-1pfy: METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH ME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pfy | ||||||
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Title | METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONYL SULPHAMOYL ADENOSINE | ||||||
Components | Methionyl-tRNA synthetase | ||||||
Keywords | LIGASE / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Crepin, T. / Schmitt, E. / Mechulam, Y. / Sampson, P.B. / Vaughan, M.D. / Honek, J.F. / Blanquet, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pfy.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pfy.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pfy_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 1pfy_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 1pfy_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1pfy_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/1pfy ftp://data.pdbj.org/pub/pdb/validation_reports/pf/1pfy | HTTPS FTP |
-Related structure data
Related structure data | 1p7pC 1pfuC 1pfvC 1pfwC 1pg0C 1pg2C 1qqtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MSP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.967 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→47 Å / Num. all: 41999 / Num. obs: 41999 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.072 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3136 / Rsym value: 0.317 / % possible all: 97.7 |
Reflection | *PLUS Num. obs: 43035 / % possible obs: 98 % / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.317 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QQT Resolution: 1.93→47 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.93→47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.95 Å /
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |