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- PDB-5uil: X-ray structure of the FdtF N-formyltransferase from Salmonella e... -

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Basic information

Entry
Database: PDB / ID: 5uil
TitleX-ray structure of the FdtF N-formyltransferase from Salmonella enterica O60 in complex with TDP-Fuc3N and tetrahydrofolate
ComponentsFormyltransferase
KeywordsTRANSFERASE / ankyrin repeat / lipopolysaccharide / O-antigen
Function / homology
Function and homology information


methionyl-tRNA formyltransferase activity / cytosol
Similarity search - Function
Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-1YJ / Chem-T3F / Formyltransferase
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWoodford, C.R. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Molecular architecture of an N-formyltransferase from Salmonella enterica O60.
Authors: Woodford, C.R. / Thoden, J.B. / Holden, H.M.
History
DepositionJan 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formyltransferase
B: Formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,00312
Polymers92,8302
Non-polymers3,17210
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-55 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.671, 72.812, 191.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Formyltransferase


Mass: 46415.215 Da / Num. of mol.: 2 / Mutation: E395A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: fdtF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: U3GK13
#2: Chemical ChemComp-1YJ / N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#3: Chemical
ChemComp-T3F / (3R,4S,5R,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate / thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminogalactose


Mass: 547.345 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM CHES 200 mM NMe4Cl 12-16% PEG 5000 10 mM TDP-Fuc3N 10 mM N-10-formyltetrahydrofolate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 18, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 46550 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4899 / Rsym value: 0.321 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uij

5uij


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.909 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 2367 5.1 %RANDOM
Rwork0.20241 ---
obs0.20577 44148 93.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--2.05 Å20 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 208 316 6992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026826
X-RAY DIFFRACTIONr_bond_other_d0.0010.026525
X-RAY DIFFRACTIONr_angle_refined_deg1.7252.0019240
X-RAY DIFFRACTIONr_angle_other_deg0.924315075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4715798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39825.203296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.442151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3771516
X-RAY DIFFRACTIONr_chiral_restr0.1030.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021506
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0732.4073190
X-RAY DIFFRACTIONr_mcbond_other2.0732.4073190
X-RAY DIFFRACTIONr_mcangle_it3.2413.63982
X-RAY DIFFRACTIONr_mcangle_other3.2413.6013983
X-RAY DIFFRACTIONr_scbond_it2.7362.7073636
X-RAY DIFFRACTIONr_scbond_other2.7362.7073637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.423.9165257
X-RAY DIFFRACTIONr_long_range_B_refined5.9119.2098150
X-RAY DIFFRACTIONr_long_range_B_other5.89119.2088064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 148 -
Rwork0.3 2697 -
obs--79.07 %

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