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- PDB-3pqs: The crystal structures of porcine pathogen ApH87_TbpB -

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Basic information

Entry
Database: PDB / ID: 3pqs
TitleThe crystal structures of porcine pathogen ApH87_TbpB
Componentstransferrin-binding protein
KeywordsLIPID BINDING PROTEIN / lipoprotein / transferrin receptor / iron acquisition / vaccine candidate / Beta barrel / Transferrin Binding / Transferrin / Outermembrane
Function / homology
Function and homology information


cell outer membrane / cell surface
Similarity search - Function
Lipocalin - #240 / Lipocalin - #250 / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / 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 / Lipocalin - #250 / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / 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
CACODYLATE ION / Transferrin-binding protein B
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCalmettes, C. / Moraes, T.F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Variations within the Transferrin Binding Site on Transferrin-binding Protein B, TbpB.
Authors: Calmettes, C. / Yu, R.H. / Silva, L.P. / Curran, D. / Schriemer, D.C. / Schryvers, A.B. / Moraes, T.F.
History
DepositionNov 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transferrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,87117
Polymers57,3531
Non-polymers1,51816
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.600, 151.300, 90.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-872-

HOH

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Components

#1: Protein transferrin-binding protein


Mass: 57352.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Strain: H87 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT SEQUENCING CONFIRMED THE RESIDUE AT THIS POSITION IS A VALINE FOR STRAIN H087 ...AUTHORS STATE THAT SEQUENCING CONFIRMED THE RESIDUE AT THIS POSITION IS A VALINE FOR STRAIN H087 USED IN THE CRYSTALLIZATION.

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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: 3.95 Å3/Da / Density % sol: 68.84 %
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

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: 1.89→50 Å / Num. obs: 53954 / % possible obs: 74 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.89-1.965.80.61923.8
1.96-2.047.30.45539.8
2.04-2.138.60.35650.4
2.13-2.2410.10.31761.5
2.24-2.3811.30.29774.7
2.38-2.5712.70.24388.7
2.57-2.8214.30.17599
2.82-3.2315.10.099100
3.23-4.0714.60.07100
4.07-5014.10.04799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å47.14 Å
Translation2.1 Å47.14 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.14 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.3 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 2658 5 %
Rwork0.16 --
obs0.162 53133 99.8 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.71 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 64.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.2004 Å2-0 Å20 Å2
2---14.7296 Å2-0 Å2
3---17.9301 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 95 498 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064204
X-RAY DIFFRACTIONf_angle_d1.0625675
X-RAY DIFFRACTIONf_dihedral_angle_d17.451578
X-RAY DIFFRACTIONf_chiral_restr0.072609
X-RAY DIFFRACTIONf_plane_restr0.004742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.30692620.27034973X-RAY DIFFRACTION100
2.1751-2.26210.26252620.22954996X-RAY DIFFRACTION100
2.2621-2.36510.24242640.20454998X-RAY DIFFRACTION100
2.3651-2.48980.24842630.18354983X-RAY DIFFRACTION100
2.4898-2.64580.24172640.17855029X-RAY DIFFRACTION100
2.6458-2.850.20142640.16775007X-RAY DIFFRACTION100
2.85-3.13680.20352660.155062X-RAY DIFFRACTION100
3.1368-3.59050.18942670.14225070X-RAY DIFFRACTION100
3.5905-4.52310.16732690.12995098X-RAY DIFFRACTION100
4.5231-47.15080.16662770.14735259X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6496-0.41220.26664.2440.19452.1513-0.05090.06850.4691-0.56410.2433-1.3837-0.40870.4003-0.17390.3236-0.04140.09590.3221-0.06780.705826.052822.384115.0544
22.7005-0.7288-0.33522.9510.83131.75-0.0547-0.19890.35980.09170.1744-0.34550.066-0.0106-0.1210.2522-0.0066-0.04350.3326-0.04850.261713.760516.420922.375
32.2693-0.2739-0.18984.7582-0.7951.7425-0.0861-0.0458-0.2118-0.48590.0919-1.07550.28940.15560.00660.41950.05660.05940.2657-0.02740.628334.7866-17.759816.2893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 26:122)A26 - 122
2X-RAY DIFFRACTION2(CHAIN A AND RESID 123:294)A123 - 294
3X-RAY DIFFRACTION3(CHAIN A AND RESID 295:528)A295 - 528

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