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

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Basic information

Entry
Database: PDB / ID: 4lxy
TitleCrystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP and 10-N-Formyl-THF
ComponentsWlaRD, a sugar 3N-formyl transferase
KeywordsTRANSFERASE / formyltransferase / formylation
Function / homologyRossmann fold - #12230 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-1YA / THYMIDINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 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

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Assembly

Deposited unit
A: WlaRD, a sugar 3N-formyl transferase
B: WlaRD, a sugar 3N-formyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0438
Polymers63,8732
Non-polymers2,1706
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-20 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.337, 65.858, 134.600
Angle α, β, γ (deg.)90.00, 109.88, 90.00
Int Tables number5
Space group name H-MC121
Detailscomposed of chains A+B

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Components

#1: Protein WlaRD, a sugar 3N-formyl transferase


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
#2: Chemical ChemComp-1YA / N-{4-[{[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}(formyl)amino]benzoyl}-L-glutamic acid


Mass: 473.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
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 10, 2013 / Details: mirrors
RadiationMonochromator: Montel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 93525 / Num. obs: 93525 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 14.6
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13710 / Rsym value: 0.364 / % possible all: 86.6

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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: 1.64→48.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.257 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22564 4704 5 %RANDOM
Rwork0.18911 ---
all0.191 93525 --
obs0.19095 88820 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.836 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.29 Å2
2--1.22 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 144 795 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194811
X-RAY DIFFRACTIONr_bond_other_d00.024630
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.9736524
X-RAY DIFFRACTIONr_angle_other_deg0.908310660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8175570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80925.738244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72315877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1071511
X-RAY DIFFRACTIONr_chiral_restr0.1310.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021172
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: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 296 -
Rwork0.317 5555 -
obs--81.6 %

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