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- PDB-3r8x: Crystal Structure of Methionyl-tRNA Formyltransferase from Yersin... -

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Basic information

Entry
Database: PDB / ID: 3r8x
TitleCrystal Structure of Methionyl-tRNA Formyltransferase from Yersinia pestis complexed with L-methionine
ComponentsMethionyl-tRNA formyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta structure / formyltransferase / cytosol
Function / homology
Function and homology information


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 / 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 ...Methionyl-tRNA formyltransferase / Methionyl-tRNA formyltransferase, N-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
METHIONINE / METHOXY-ETHOXYL / Methionyl-tRNA formyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 Å
AuthorsMaltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Methionyl-tRNA Formyltransferase from Yersinia pestis complexed with L-methionine
Authors: Maltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0717
Polymers34,4491
Non-polymers6236
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methionyl-tRNA formyltransferase
hetero molecules

A: Methionyl-tRNA formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,14214
Polymers68,8972
Non-polymers1,24512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area3540 Å2
ΔGint-11 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.750, 62.750, 172.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methionyl-tRNA formyltransferase


Mass: 34448.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: fmt, y4022, YPO0241, YP_0239 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q8ZJ80, methionyl-tRNA formyltransferase

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Non-polymers , 5 types, 148 molecules

#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MOE / METHOXY-ETHOXYL


Mass: 75.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris, 20 % PEGMME2000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 17092 / Num. obs: 17092 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 32.89 Å2 / Rsym value: 0.142 / Net I/σ(I): 6.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 819 / Rsym value: 0.751 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_601)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FMT

1fmt


Resolution: 2.256→42.974 Å / SU ML: 0.28 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 858 5.05 %random
Rwork0.177 ---
all0.18 16993 --
obs0.18 16993 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.06 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.0027 Å20 Å2-0 Å2
2--10.0027 Å2-0 Å2
3----8.0519 Å2
Refinement stepCycle: LAST / Resolution: 2.256→42.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 40 142 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012553
X-RAY DIFFRACTIONf_angle_d1.3953482
X-RAY DIFFRACTIONf_dihedral_angle_d15.438956
X-RAY DIFFRACTIONf_chiral_restr0.1394
X-RAY DIFFRACTIONf_plane_restr0.009456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2562-2.39750.29111410.2182596273799
2.3975-2.58260.27461440.1992609275399
2.5826-2.84250.26561430.195626452788100
2.8425-3.25370.25741460.17726592805100
3.2537-4.09880.20961400.154227162856100
4.0988-42.98210.19711440.174929103054100
Refinement TLS params.Method: refined / Origin x: -14.373 Å / Origin y: -21.9141 Å / Origin z: -9.4952 Å
111213212223313233
T0.0627 Å2-0.0328 Å2-0.0042 Å2-0.1895 Å20.0523 Å2--0.0838 Å2
L-0.1834 °2-0.0302 °20.2326 °2-0.2987 °2-0.4198 °2--1.176 °2
S-0.0187 Å °0.0724 Å °-0.0038 Å °0.0197 Å °-0.0573 Å °-0.0344 Å °-0.1497 Å °0.2169 Å °0.0138 Å °
Refinement TLS groupSelection details: chain A

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