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- PDB-4yfy: X-ray structure of the Viof N-formyltransferase from Providencia ... -

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Basic information

Entry
Database: PDB / ID: 4yfy
TitleX-ray structure of the Viof N-formyltransferase from Providencia alcalifaciens O30 in complex with THF and TDP-Qui4N
ComponentsVioF
KeywordsTRANSFERASE / lipopolysaccharide O-antigen
Function / homology
Function and homology information


methionyl-tRNA formyltransferase activity / cytosol
Similarity search - Function
N-formyltransferase dimerization C-terminal domain / N-formyltransferase dimerization C-terminal domain / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
dTDP-4-amino-4,6-dideoxyglucose / Chem-1YJ / VioF
Similarity search - Component
Biological speciesProvidencia alcalifaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGenthe, N.A. / Thoden, J.B. / Benning, M.M. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2015
Title: Molecular structure of an N-formyltransferase from Providencia alcalifaciens O30.
Authors: Genthe, N.A. / Thoden, J.B. / Benning, M.M. / Holden, H.M.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Structure summary
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VioF
B: VioF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4388
Polymers59,3552
Non-polymers2,0836
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-11 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.000, 132.000, 161.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-303-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein VioF


Mass: 29677.713 Da / Num. of mol.: 2 / Fragment: residues 9-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia alcalifaciens (bacteria) / Gene: vioF / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettas2(DE3) / References: UniProt: M9P0Q2

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Non-polymers , 5 types, 454 molecules

#2: Chemical ChemComp-0FX / dTDP-4-amino-4,6-dideoxyglucose


Mass: 547.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.04 % / Description: six-sided stellate rods
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-10% PEG-8000, 1 M tetramethylammonium chloride 100 mM Hepes

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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 23, 2014
RadiationMonochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 42792 / Num. obs: 42792 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFV

4yfv


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.978 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24391 2161 5.1 %RANDOM
Rwork0.18658 ---
obs0.18948 40605 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.37 Å20 Å2
2--0.37 Å20 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 139 448 4543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194185
X-RAY DIFFRACTIONr_bond_other_d00.023988
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9995673
X-RAY DIFFRACTIONr_angle_other_deg0.89139212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0135482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03726.176204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78215769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.302158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024651
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02939
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 154 -
Rwork0.246 2908 -
obs--97.27 %

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