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- PDB-5vyt: Crystal structure of the WbkC N-formyltransferase (F142A variant)... -

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Basic information

Entry
Database: PDB / ID: 5vyt
TitleCrystal structure of the WbkC N-formyltransferase (F142A 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 / GDP-mannose 4,6-dehydratase activity / 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-FON / GUANOSINE-5'-DIPHOSPHATE / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
D: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,68014
Polymers116,9424
Non-polymers3,73710
Water5,513306
1
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)60,3046
Polymers58,4712
Non-polymers1,8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-27 kcal/mol
Surface area21850 Å2
MethodPISA
2
C: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
D: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3758
Polymers58,4712
Non-polymers1,9046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-42 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.315, 68.021, 236.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29235.553 Da / Num. of mol.: 4 / Mutation: D78A, F142A
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
#2: 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.: 4 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13-15% PEG5000, 2% glycerol, 5 mM GDP-perosamine, 5 mM folinic acid, 100 mM MES

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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: Sep 23, 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: 54309 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5278 / Rsym value: 0.412 / % possible all: 80.6

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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→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.037 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26779 2687 4.9 %RANDOM
Rwork0.20213 ---
obs0.20537 51622 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7950 0 194 306 8450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198357
X-RAY DIFFRACTIONr_bond_other_d0.0020.027884
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.98411342
X-RAY DIFFRACTIONr_angle_other_deg0.992318060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63951002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20222.689383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.316151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6661574
X-RAY DIFFRACTIONr_chiral_restr0.0860.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219391
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022057
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_it1.8632.7454023
X-RAY DIFFRACTIONr_mcbond_other1.8572.7424019
X-RAY DIFFRACTIONr_mcangle_it2.9984.1035017
X-RAY DIFFRACTIONr_mcangle_other2.9974.1035016
X-RAY DIFFRACTIONr_scbond_it2.1813.064334
X-RAY DIFFRACTIONr_scbond_other2.1783.0574330
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4884.4986319
X-RAY DIFFRACTIONr_long_range_B_refined5.13522.4359604
X-RAY DIFFRACTIONr_long_range_B_other5.11422.4419542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 117 -
Rwork0.335 2836 -
obs--72.09 %

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