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- PDB-4ly3: Crystal structure of WlaRD, a sugar 3N-formyl transferase in the ... -

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Basic information

Entry
Database: PDB / ID: 4ly3
TitleCrystal structure of WlaRD, a sugar 3N-formyl transferase in the presence of dTPD-Qui3N, dTDP-Qui3NFo, and THF
ComponentsWlaRD a sugar 3N formyltransferase
KeywordsTRANSFERASE / formyltransferase
Function / homologyRossmann fold - #12230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / Chem-1YJ / Chem-T3Q / :
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThoden, J.B. / Goneau, M.-F. / Gilbert, M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2013
Title: Structure of a sugar N-formyltransferase from Campylobacter jejuni.
Authors: Thoden, J.B. / Goneau, M.F. / Gilbert, M. / Holden, H.M.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: WlaRD a sugar 3N formyltransferase
B: WlaRD a sugar 3N formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3058
Polymers63,8732
Non-polymers2,4326
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint8 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.003, 65.552, 134.501
Angle α, β, γ (deg.)90.00, 109.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein WlaRD a sugar 3N formyltransferase


Mass: 31936.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: 81116 / Gene: C8J_1081 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A8FMJ3

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Non-polymers , 5 types, 615 molecules

#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-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.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-1YF / [(2R,3R,4S,5S,6R)-4-formamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 575.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11-15% PEG 8000, 200 mM NaCl, 5 mM TDP, 5 mM N-5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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 20, 2013 / Details: mirrors
RadiationMonochromator: montel optics / 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: 58443 / Num. obs: 58443 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
REFMAC5.7.0029refinement
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LXQ

4lxq


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.258 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22617 2940 5 %RANDOM
Rwork0.17758 ---
obs0.17999 55503 91.9 %-
all-58443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.06 Å2
2--0.82 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 162 609 5243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194748
X-RAY DIFFRACTIONr_bond_other_d0.0010.024556
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9776424
X-RAY DIFFRACTIONr_angle_other_deg0.881310480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4645546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69225.714238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62615854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.251510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025312
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021147
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: 1.885→1.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 178 -
Rwork0.259 2987 -
obs--67.51 %

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