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- PDB-2fmt: METHIONYL-TRNAFMET FORMYLTRANSFERASE COMPLEXED WITH FORMYL-METHIO... -

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Basic information

Entry
Database: PDB / ID: 2fmt
TitleMETHIONYL-TRNAFMET FORMYLTRANSFERASE COMPLEXED WITH FORMYL-METHIONYL-TRNAFMET
Components
  • FORMYL-METHIONYL-TRNAFMET2
  • METHIONYL-TRNA FMET FORMYLTRANSFERASE
KeywordsCOMPLEX (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
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
N-FORMYLMETHIONINE / RNA / RNA (> 10) / Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.8 Å
AuthorsSchmitt, E. / Mechulam, Y. / Blanquet, S.
CitationJournal: 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
DepositionJul 29, 1998Processing site: NDB
Revision 1.0Jul 29, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Derived calculations / Source and taxonomy
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
C: FORMYL-METHIONYL-TRNAFMET2
D: FORMYL-METHIONYL-TRNAFMET2
A: METHIONYL-TRNA FMET FORMYLTRANSFERASE
B: METHIONYL-TRNA FMET FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2118
Polymers117,8084
Non-polymers4034
Water1,49583
1
C: FORMYL-METHIONYL-TRNAFMET2
A: METHIONYL-TRNA FMET FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1064
Polymers58,9042
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: FORMYL-METHIONYL-TRNAFMET2
B: METHIONYL-TRNA FMET FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1064
Polymers58,9042
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.710, 68.060, 86.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.97939, -0.20195, -0.00234), (0.20193, 0.97937, -0.00813), (0.00394, 0.00749, 0.99996)6.31224, -48.79334, 0.7839
2given(0.99474, -0.1024, -0.00348), (0.10227, 0.99438, -0.02719), (0.00625, 0.02669, 0.99962)3.90927, -42.125, 0.04122
DetailsTHE 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.

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Components

#1: RNA chain FORMYL-METHIONYL-TRNAFMET2 / INITIATOR TRNA


Mass: 24832.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.51 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.6 / Details: pH 6.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 %mPEG500011
20.2 Mammonium sulfate11
38 %ethylene glycol11
40.060 mMprotein11
50.066 mMformylase11
610 mM11MgCl2
750 mM11KCl
850 mMMES-Na11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.3Crefinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: SIR
Starting model: PDB ENTRY 1FMT

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1528 6 %RANDOM
Rwork0.247 ---
obs0.247 26136 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.1 Å2 / ksol: 0.234 e/Å3
Displacement parametersBiso mean: 62.7 Å2
Baniso -1Baniso -2Baniso -3
1--16.23 Å20 Å20 Å2
2---7.43 Å20 Å2
3---26.67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 3310 2 83 8179
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.72
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.72
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it3.92.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.1550
22X-RAY DIFFRACTION0.2650
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.428 135 3.7 %
Rwork0.362 2171 -
obs--63.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3ION.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION4ION.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.72
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27

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