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Yorodumi- PDB-2fmt: METHIONYL-TRNAFMET FORMYLTRANSFERASE COMPLEXED WITH FORMYL-METHIO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fmt | ||||||
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Title | METHIONYL-TRNAFMET FORMYLTRANSFERASE COMPLEXED WITH FORMYL-METHIONYL-TRNAFMET | ||||||
Components |
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Keywords | COMPLEX (METHYLTRANSFERASE/TRNA) / COMPLEX (METHYLTRANSFERASE-TRNA) / FORMYLTRANSFERASE / INITIATION OF TRANSLATION / COMPLEX (METHYLTRANSFERASE-TRNA) complex | ||||||
Function / homology | Function and homology information charged-tRNA amino acid modification / methionyl-tRNA formyltransferase / conversion of methionyl-tRNA to N-formyl-methionyl-tRNA / methionyl-tRNA formyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.8 Å | ||||||
Authors | Schmitt, E. / Mechulam, Y. / Blanquet, S. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet. Authors: Schmitt, E. / Panvert, M. / Blanquet, S. / Mechulam, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fmt.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fmt.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/2fmt ftp://data.pdbj.org/pub/pdb/validation_reports/fm/2fmt | HTTPS FTP |
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-Related structure data
Related structure data | 1fmtS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Details | THE BIOLOGICALLY ACTIVE COMPLEX CORRESPONDS TO EITHER CHAINS A AND C, OR CHAINS B AND D. THE COORDINATES FOR CHAINS A AND C ARE MORE ACCURATE. |
-Components
#1: RNA chain | Mass: 24832.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | Mass: 34071.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K37 / Cellular location: CYTOPLASM / Gene: FMT / Plasmid: PUCFATG / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM101TR References: UniProt: P23882, methionyl-tRNA formyltransferase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 / Details: pH 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 29912 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 78 Å2 / Rsym value: 0.051 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.351 / % possible all: 99.6 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Rmerge(I) obs: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: SIR Starting model: PDB ENTRY 1FMT Resolution: 2.8→19 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE POSITIONS OF BASES 1, 16 - 18 AND 37 IN CHAINS C AND D ARE TENTATIVE.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.1 Å2 / ksol: 0.234 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.8→2.93 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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