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- PDB-4o4x: Crystal structure of the vaccine antigen Transferrin Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 4o4x
TitleCrystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) double mutant Tyr-167-Ala and Trp-176-Ala from Haemophilus parasuis Hp5
ComponentsTbpB
KeywordsMETAL TRANSPORT / Structure-based vaccine design / transferrin receptor / iron acquisition / host pathogen interaction / surface lipoprotein
Function / homology
Function and homology information


Lipocalin - #240 / 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 ...Lipocalin - #240 / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHaemophilus parasuis (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 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Oct 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: TbpB
B: TbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,40422
Polymers116,5912
Non-polymers1,81220
Water90150
1
A: TbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,34713
Polymers58,2961
Non-polymers1,05212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0569
Polymers58,2961
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)239.890, 42.240, 114.020
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TbpB


Mass: 58295.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parasuis (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2UKY6*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08 M potassium phosphate monobasic, 18% PEG 8000, 20% 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: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→42.182 Å / Num. obs: 26504 / Biso Wilson estimate: 57.75 Å2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→42.182 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.41 / σ(F): 1.35 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 1293 4.99 %
Rwork0.216 --
obs0.2169 25890 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.5643 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7764 0 105 50 7919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058003
X-RAY DIFFRACTIONf_angle_d0.8410773
X-RAY DIFFRACTIONf_dihedral_angle_d13.3912918
X-RAY DIFFRACTIONf_chiral_restr0.0381144
X-RAY DIFFRACTIONf_plane_restr0.0031397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.01610.39841380.35912589X-RAY DIFFRACTION94
3.0161-3.15340.32141410.3042676X-RAY DIFFRACTION100
3.1534-3.31950.25471370.2652714X-RAY DIFFRACTION100
3.3195-3.52740.26881510.23822739X-RAY DIFFRACTION100
3.5274-3.79960.23551430.21522735X-RAY DIFFRACTION100
3.7996-4.18170.23651430.20032727X-RAY DIFFRACTION100
4.1817-4.78610.19251440.17562744X-RAY DIFFRACTION100
4.7861-6.02710.20021450.18632801X-RAY DIFFRACTION100
6.0271-42.18640.2011510.19582872X-RAY DIFFRACTION100

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