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- PDB-4o3z: Crystal structure of the vaccine antigen Transferrin Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 4o3z
TitleCrystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant Tyr-95-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 / Resolution: 2.9 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 27, 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)58,06810
Polymers57,4051
Non-polymers6649
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.100, 149.200, 90.930
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: Y95A
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.99 Å3/Da / Density % sol: 69.18 %
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: 2.9→46.671 Å / Num. obs: 20736 / Biso Wilson estimate: 61.03 Å2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.671 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8832 / SU ML: 0.29 / σ(F): 1.99 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 1037 5 %
Rwork0.1841 19699 -
obs0.1846 20736 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.98 Å2 / Biso mean: 69.071 Å2 / Biso min: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 44 61 3977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063976
X-RAY DIFFRACTIONf_angle_d0.9745344
X-RAY DIFFRACTIONf_chiral_restr0.036575
X-RAY DIFFRACTIONf_plane_restr0.003705
X-RAY DIFFRACTIONf_dihedral_angle_d13.841463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-3.05290.25151450.250727722917
3.0529-3.24410.23541470.240727892936
3.2441-3.49450.27271460.214527822928
3.4945-3.84610.19731470.194727812928
3.8461-4.40220.17891470.16728122959
4.4022-5.54490.15721490.155228192968
5.5449-46.67750.17621560.168229443100

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