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- PDB-5uim: X-ray structure of the FdtF N-formyltransferase from salmonella e... -

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Basic information

Entry
Database: PDB / ID: 5uim
TitleX-ray structure of the FdtF N-formyltransferase from salmonella enteric O60 in complex with folinic acid and TDP-Qui3N
ComponentsFormyltransferaseTransferase
KeywordsTRANSFERASE / ankyrin repeat / lipopolysaccharide / O-antigen
Function / homology
Function and homology information


hydroxymethyl-, formyl- and related transferase activity / biosynthetic process
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 repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-FON / : / Chem-T3Q / THYMIDINE-5'-DIPHOSPHATE / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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)95,47912
Polymers92,8302
Non-polymers2,64910
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-59 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.236, 58.406, 106.781
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Formyltransferase / Transferase


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

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Non-polymers , 6 types, 240 molecules

#2: Chemical ChemComp-T3Q / [(3R,4S,5S,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-aminoglucose


Mass: 547.345 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#5: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM CHES 200 mM NMe4Cl 13-17% PEG 5000 10 mM folinic acid 10 mM TDP-Qui3N

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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: Jun 6, 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: 42547 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4812 / Rsym value: 0.295 / % possible all: 86.6

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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: 0.946 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.469 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.248 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2149 5.1 %RANDOM
Rwork0.19451 ---
obs0.19799 40390 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.471 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-1.11 Å2
2--2.01 Å20 Å2
3----1.56 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 169 230 6863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026787
X-RAY DIFFRACTIONr_bond_other_d0.0010.026514
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9949186
X-RAY DIFFRACTIONr_angle_other_deg0.902315048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5115799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76925.219297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7651516
X-RAY DIFFRACTIONr_chiral_restr0.0970.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021513
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_it2.6733.0173187
X-RAY DIFFRACTIONr_mcbond_other2.6733.0173188
X-RAY DIFFRACTIONr_mcangle_it4.0324.5163980
X-RAY DIFFRACTIONr_mcangle_other4.0334.5163981
X-RAY DIFFRACTIONr_scbond_it3.3423.3483600
X-RAY DIFFRACTIONr_scbond_other3.2793.3443592
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1384.8565191
X-RAY DIFFRACTIONr_long_range_B_refined6.89824.1388126
X-RAY DIFFRACTIONr_long_range_B_other6.89824.1398127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 150 -
Rwork0.315 2693 -
obs--86 %

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