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- PDB-5vys: Crystal structure of the WbkC N-formyltransferase (C47S variant) ... -

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Basic information

Entry
Database: PDB / ID: 5vys
TitleCrystal structure of the WbkC N-formyltransferase (C47S variant) from Brucella melitensis
ComponentsGdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
KeywordsTRANSFERASE / brucellosis / deoxysugar
Function / homology
Function and homology information


GDP-perosamine N-formyltransferase / methionyl-tRNA formyltransferase activity / lipopolysaccharide biosynthetic process / cytosol
Similarity search - Function
Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily
Similarity search - Domain/homology
Chem-1YJ / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE / GDP-perosamine N-formyltransferase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRiegert, A.S. / Chantigian, D.P. / 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: Biochemistry / Year: 2017
Title: Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis.
Authors: Riegert, A.S. / Chantigian, D.P. / Thoden, J.B. / Tipton, P.A. / Holden, H.M.
History
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
B: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7148
Polymers58,5912
Non-polymers2,1236
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-28 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.927, 65.927, 234.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase


Mass: 29295.584 Da / Num. of mol.: 2 / Mutation: C47S, D78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI1418 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: F8WJP6, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases, GDP-mannose 4,6-dehydratase

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Non-polymers , 5 types, 256 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 19-25%PEG-5000, 5 mM GDP-perosamine, 5 mM folinic acid, 100 mM MOPS

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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: Aug 25, 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: 27237 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4 / Num. unique obs: 3263 / Rsym value: 0.405 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vyr

5vyr


Resolution: 2.2→29.965 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.214 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25784 1371 5 %RANDOM
Rwork0.18507 ---
obs0.18874 25866 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 104 250 4267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194134
X-RAY DIFFRACTIONr_bond_other_d0.0020.023870
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9855617
X-RAY DIFFRACTIONr_angle_other_deg0.98438870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91922.865192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30615657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.891535
X-RAY DIFFRACTIONr_chiral_restr0.0930.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214622
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021009
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_it22.6891977
X-RAY DIFFRACTIONr_mcbond_other1.9932.6891976
X-RAY DIFFRACTIONr_mcangle_it3.1614.0222467
X-RAY DIFFRACTIONr_mcangle_other3.1614.0232468
X-RAY DIFFRACTIONr_scbond_it2.4283.0542157
X-RAY DIFFRACTIONr_scbond_other2.4263.0532157
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9524.4853149
X-RAY DIFFRACTIONr_long_range_B_refined5.57222.5734930
X-RAY DIFFRACTIONr_long_range_B_other5.57322.584931
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
Rfree0.364 100 -
Rwork0.276 1812 -
obs--97.85 %

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