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- PDB-5uij: X-ray structure of The FdtF N-formyltransferase from Salmonella e... -

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Basic information

Entry
Database: PDB / ID: 5uij
TitleX-ray structure of The FdtF N-formyltransferase from Salmonella enteric O60 in complex with TDP
ComponentsFormyltransferase
KeywordsTRANSFERASE / ankyrin / o-antigen / lipopolysaccharide
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
THYMIDINE-5'-DIPHOSPHATE / Formyltransferase
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThoden, J.B. / Woodford, C.R. / 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 / _struct_conn.ptnr2_symmetry

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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)94,61612
Polymers92,8302
Non-polymers1,78610
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-91 kcal/mol
Surface area36090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.910, 64.757, 97.757
Angle α, β, γ (deg.)90.00, 90.54, 90.00
Int Tables number4
Space group name H-MP1211

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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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM MOPS 15-18% PEG 3350 5 mM TDP

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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 5, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→97.75 Å / Num. obs: 70013 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9252 / Rsym value: 0.278 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xcz

4xcz


Resolution: 1.9→97.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.115 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23126 3552 5.1 %RANDOM
Rwork0.18081 ---
obs0.18332 66447 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.52 Å2
2--1.44 Å20 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.9→97.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 109 555 7127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026714
X-RAY DIFFRACTIONr_bond_other_d0.0010.026451
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.9839078
X-RAY DIFFRACTIONr_angle_other_deg0.944314903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19525.203296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.043151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0771516
X-RAY DIFFRACTIONr_chiral_restr0.1240.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021484
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_it2.6792.3173184
X-RAY DIFFRACTIONr_mcbond_other2.6792.3173183
X-RAY DIFFRACTIONr_mcangle_it3.4653.4573978
X-RAY DIFFRACTIONr_mcangle_other3.4653.4583979
X-RAY DIFFRACTIONr_scbond_it4.0582.7553530
X-RAY DIFFRACTIONr_scbond_other4.0582.7553530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8483.9415098
X-RAY DIFFRACTIONr_long_range_B_refined7.09919.6418388
X-RAY DIFFRACTIONr_long_range_B_other7.09919.6428389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 252 -
Rwork0.268 4277 -
obs--84.26 %

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