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- PDB-4o49: Crystal structure of the vaccine antigen Transferrin Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 4o49
TitleCrystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant Tyr-174-Ala from Actinobacillus pleuropneumoniae H87
ComponentsOuter membrane protein; transferrin-binding protein
KeywordsMETAL TRANSPORT / Structure-based vaccine design / transferrin receptor / iron acquisition / host pathogen interaction / surface lipoprotein
Function / homology
Function and homology information


cell outer membrane / cell surface
Similarity search - Function
Lipocalin - #240 / Transferrin-binding protein B, N-lobe handle / Lipocalin - #250 / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B ...Lipocalin - #240 / Transferrin-binding protein B, N-lobe handle / Lipocalin - #250 / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Transferrin-binding protein B
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsCalmettes, C. / Yu, R.H. / Schryvers, A.B. / Moraes, T.F.
CitationJournal: Infect.Immun. / Year: 2015
Title: Nonbinding site-directed mutants of transferrin binding protein B exhibit enhanced immunogenicity and protective capabilities.
Authors: Frandoloso, R. / Martinez-Martinez, S. / Calmettes, C. / Fegan, J. / Costa, E. / Curran, D. / Yu, R.H. / Gutierrez-Martin, C.B. / Rodriguez-Ferri, E.F. / Moraes, T.F. / Schryvers, A.B.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Outer membrane protein; transferrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7336
Polymers57,4051
Non-polymers3285
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.800, 150.400, 93.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Outer membrane protein; transferrin-binding protein


Mass: 57404.668 Da / Num. of mol.: 1 / Fragment: UNP residues 25-547 / Mutation: Y174A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Gene: tfbA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44167
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M sodium acetate, 0.08 M calcium cacodylate, 23% PEG 3350, 15% glycerol, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→46.902 Å / Num. obs: 32675 / Biso Wilson estimate: 45.52 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.902 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8288 / SU ML: 0.33 / σ(F): 2 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 1510 4.62 %
Rwork0.197 31154 -
obs0.1973 32664 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.66 Å2 / Biso mean: 57.03 Å2 / Biso min: 18.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 22 135 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054032
X-RAY DIFFRACTIONf_angle_d0.8225446
X-RAY DIFFRACTIONf_chiral_restr0.035587
X-RAY DIFFRACTIONf_plane_restr0.002726
X-RAY DIFFRACTIONf_dihedral_angle_d13.2031506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58070.39811330.39182751288499
2.5807-2.67290.3351360.321128012937100
2.6729-2.77990.34911360.294927902926100
2.7799-2.90640.28621360.257728152951100
2.9064-3.05970.23111360.229728062942100
3.0597-3.25130.2331370.215728242961100
3.2513-3.50230.20681360.197328162952100
3.5023-3.85460.17981380.187828462984100
3.8546-4.4120.16941380.15928562994100
4.412-5.55720.15931390.14628683007100
5.5572-46.91070.15481450.159229813126100

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