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- PDB-4o3w: Crystal structure of the vaccine antigen Transferrin Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 4o3w
TitleCrystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant Tyr-63-Ala from Actinobacillus suis H57
ComponentsTransferrin binding protein B
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
Transferrin-binding protein B
Similarity search - Component
Biological speciesActinobacillus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transferrin binding protein B
B: Transferrin binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4126
Polymers126,0392
Non-polymers3724
Water10,971609
1
A: Transferrin binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2043
Polymers63,0201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transferrin binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2083
Polymers63,0201
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.810, 74.510, 106.600
Angle α, β, γ (deg.)90.000, 105.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transferrin binding protein B / Transferrin-binding protein B


Mass: 63019.609 Da / Num. of mol.: 2 / Fragment: UNP residues 27-596 / Mutation: F63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus suis (bacteria) / Gene: tbpB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83UA7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.4 M lithium sulfate, 17% PEG 3350, 20% glycerol, pH 5.5, 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: 2.1→46.279 Å / Num. obs: 74646 / Biso Wilson estimate: 28.31 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: 2.1→46.279 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / σ(F): 1.99 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1851 2.53 %
Rwork0.1903 71395 -
obs0.1907 73246 91.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.3 Å2 / Biso mean: 47.5664 Å2 / Biso min: 10.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8409 0 23 609 9041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088606
X-RAY DIFFRACTIONf_angle_d1.12311574
X-RAY DIFFRACTIONf_chiral_restr0.0531221
X-RAY DIFFRACTIONf_plane_restr0.0051531
X-RAY DIFFRACTIONf_dihedral_angle_d14.2653187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15680.2899890.2733441353058
2.1568-2.22030.27061040.24063998410267
2.2203-2.29190.25381200.2384625474578
2.2919-2.37380.23371360.21725267540388
2.3738-2.46890.23741510.21155831598297
2.4689-2.58120.2231550.208559776132100
2.5812-2.71730.21431560.215460046160100
2.7173-2.88750.2341550.216759896144100
2.8875-3.11040.22021560.211960116167100
3.1104-3.42330.22221560.193160126168100
3.4233-3.91850.18981570.174460376194100
3.9185-4.9360.1571560.151760336189100
4.936-46.29050.18351600.166561706330100

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