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- PDB-5vyr: Crystal structure of the WbkC formyl transferase from Brucella me... -

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Basic information

Entry
Database: PDB / ID: 5vyr
TitleCrystal structure of the WbkC formyl transferase from Brucella melitensis
ComponentsGdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
KeywordsTRANSFERASE / N-formyltransferase / 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-B62 / GUANOSINE / GDP-perosamine N-formyltransferase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 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

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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)59,9339
Polymers58,6232
Non-polymers1,3107
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-29 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.875, 65.875, 233.140
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: 29311.646 Da / Num. of mol.: 2 / Mutation: 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, 386 molecules

#2: Chemical ChemComp-B62 / (6R)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one


Mass: 181.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N5O
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18-22% PEG-5000, 5 mM GDP, 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: Jun 12, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 57143 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8645 / Rsym value: 0.308 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.648 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2807 4.9 %RANDOM
Rwork0.18478 ---
obs0.18721 54336 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 73 379 4326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194114
X-RAY DIFFRACTIONr_bond_other_d0.0010.023861
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9735597
X-RAY DIFFRACTIONr_angle_other_deg0.86538856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0045508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96423.01196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8781535
X-RAY DIFFRACTIONr_chiral_restr0.1080.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
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_it2.1681.9091978
X-RAY DIFFRACTIONr_mcbond_other2.1681.9081977
X-RAY DIFFRACTIONr_mcangle_it3.0782.8442471
X-RAY DIFFRACTIONr_mcangle_other3.0782.8452472
X-RAY DIFFRACTIONr_scbond_it3.0182.3272136
X-RAY DIFFRACTIONr_scbond_other3.0172.3272136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.683.3643116
X-RAY DIFFRACTIONr_long_range_B_refined6.42917.2145316
X-RAY DIFFRACTIONr_long_range_B_other6.42917.2215317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 186 -
Rwork0.286 3873 -
obs--96.9 %

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