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- PDB-1fmt: METHIONYL-TRNAFMET FORMYLTRANSFERASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1fmt
TitleMETHIONYL-TRNAFMET FORMYLTRANSFERASE FROM ESCHERICHIA COLI
ComponentsMETHIONYL-TRNA FMET FORMYLTRANSFERASE
KeywordsFORMYLTRANSFERASE / INITIATOR TRNA / TRANSLATION INITIATION
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
Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-terminal domain / Methionyl-tRNA formyltransferase, C-terminal domain / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain ...Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-terminal domain / Methionyl-tRNA formyltransferase, C-terminal domain / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsSchmitt, E. / Mechulam, Y.
CitationJournal: EMBO J. / Year: 1996
Title: Structure of crystalline Escherichia coli methionyl-tRNA(f)Met formyltransferase: comparison with glycinamide ribonucleotide formyltransferase.
Authors: Schmitt, E. / Blanquet, S. / Mechulam, Y.
History
DepositionOct 13, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONYL-TRNA FMET FORMYLTRANSFERASE
B: METHIONYL-TRNA FMET FORMYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)68,1422
Polymers68,1422
Non-polymers00
Water2,720151
1
A: METHIONYL-TRNA FMET FORMYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)34,0711
Polymers34,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METHIONYL-TRNA FMET FORMYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)34,0711
Polymers34,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.040, 151.040, 81.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.141, -0.8341, -0.5333), (-0.0802, 0.5273, -0.8459), (0.9868, 0.162, 0.0075)
Vector: 141.50841, 115.9274, 44.2644)

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Components

#1: Protein METHIONYL-TRNA FMET FORMYLTRANSFERASE / 10-FORMYLTETRAHYDROFOLATE L-METHIONYL TRNAFMET FORMYLTRANSFERASE


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 4 Å3/Da / Density % sol: 72 %
Crystal growpH: 7.3
Details: PROTEIN WAS CRYSTALLIZED IN 45-52% AMMONIUM SULFATE, 100 MM KCL, 2-10 % GLYCEROL, 10 MM POTASSIUM PHOSPHATE PH7.3
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, hanging drop
Details: Schmitt, E., (1996) Proteins. Struct.Funct. Genet., 25, 139.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
145-52 %ammonium salfate1drop
210 mMpotassium phosphate1drop
3100 mM1dropKCl
410 mM2-mercaptoethanol1drop
52-10 %glycerol1drop
610-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.902
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1995
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.902 Å / Relative weight: 1
ReflectionResolution: 1.99→27 Å / Num. obs: 71246 / % possible obs: 96.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 8
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.252 / % possible all: 77.7
Reflection
*PLUS
Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6792 10 %RANDOM
Rwork0.214 ---
obs0.214 67197 92.7 %-
Displacement parametersBiso mean: 28.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 0 151 6159
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2.32
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.99→2.08 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.288 745 10 %
Rwork0.276 6415 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43

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