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- PDB-3pqu: The crystal structures of porcine pathogen AsH57_TbpB -

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Basic information

Entry
Database: PDB / ID: 3pqu
TitleThe crystal structures of porcine pathogen AsH57_TbpB
ComponentsTransferrin binding protein B
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
Transferrin-binding protein B
Similarity search - Component
Biological speciesActinobacillus suis (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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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: Transferrin binding protein B
B: Transferrin binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3647
Polymers125,9032
Non-polymers4605
Water16,033890
1
A: Transferrin binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2284
Polymers62,9521
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transferrin binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1363
Polymers62,9521
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 74.470, 106.400
Angle α, β, γ (deg.)90.000, 105.700, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND ((RESSEQ 37:67) OR (RESSEQ 71:224) OR (RESSEQ...A0
211CHAIN B AND ((RESSEQ 37:67) OR (RESSEQ 71:224) OR (RESSEQ...B0

NCS oper: (Code: given
Matrix: (0.851745, 0.01208, 0.523817), (0.010727, -0.999927, 0.005618), (0.523847, 0.000834, -0.851812)
Vector: -7.60348, -27.823601, 27.4865)

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Components

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


Mass: 62951.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus suis (bacteria) / Strain: H57 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 55.22 %
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

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: 1.82→50 Å / Num. obs: 79607 / % possible obs: 63.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Χ2: 1.235 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.82-1.8912120.6241.8
1.89-1.961.310700.7078.80.625
1.96-2.051.631570.81426.10.402
2.05-2.16256770.84346.70.351
2.16-2.292.584670.82269.80.338
2.29-2.473.1105850.85586.80.295
2.47-2.723.8114480.86393.80.24
2.72-3.114.2120120.94498.60.139
3.11-3.924.8122691.5151000.078
3.92-505.1124151.76799.80.054

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å46.25 Å
Translation2.2 Å46.25 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
Starting model: PDB entry 3HOL

3hol


Resolution: 2.1→44.755 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8865 / SU ML: 0.27 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 3981 5 %
Rwork0.1721 --
obs0.1744 77312 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.138 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 205 Å2 / Biso mean: 50.1521 Å2 / Biso min: 4.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.0597 Å2-0 Å2-0.7428 Å2
2---3.728 Å20 Å2
3----1.3317 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8468 0 30 890 9388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078792
X-RAY DIFFRACTIONf_angle_d1.07111846
X-RAY DIFFRACTIONf_chiral_restr0.0781249
X-RAY DIFFRACTIONf_plane_restr0.0041568
X-RAY DIFFRACTIONf_dihedral_angle_d16.3093245
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3502X-RAY DIFFRACTIONPOSITIONAL0.038
12B3502X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.26563940.21497479787399
2.1751-2.26210.24593930.19447470786399
2.2621-2.36510.24773940.188774957889100
2.3651-2.48980.24323970.179875367933100
2.4898-2.64570.2553960.185875337929100
2.6457-2.850.22193990.1775717970100
2.85-3.13670.21613980.163575657963100
3.1367-3.59050.19474000.162175947994100
3.5905-4.52290.18794010.144276208021100
4.5229-44.76520.19424090.16877638172100
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)
10.03740.0071-0.20910.6660.03481.13330.0376-0.0486-0.02640.2181-0.01980.19770.1316-0.17-0.00850.1452-0.04460.01090.11810.02040.134215.4561-16.179553.623
20.84880.15840.08511.43190.06361.2132-0.06080.11050.0596-0.03150.0396-0.0325-0.04330.00560.01840.0292-0.01180.010.02730.00780.011226.1127-10.341841.7594
31.1830.4193-0.39261.8101-0.31781.8312-0.03860.23860.2531-0.0137-0.05250.7-0.0611-0.88130.12620.0113-0.0346-0.06240.6135-0.07260.3483-14.8599-16.484336.349
40.3750.2283-0.65460.3762-0.20481.29060.01060.14360.063-0.23570.05430.0879-0.124-0.1801-0.07530.23170.00920.02250.17290.04530.164633.4074-11.4072-10.1569
50.9347-0.3539-0.11811.59430.08311.3443-0.0934-0.1114-0.10650.10690.1273-0.00070.0608-0.02340.00890.08260.00210.04430.03060.03080.020436.41-17.04265.697
60.25130.0427-0.36651.7626-0.00345.4526-0.09620.1204-0.0403-0.07060.19590.59310.344-2.0761-0.23930.0212-0.0807-0.07230.88970.14430.2671-1.0372-11.3239-10.9509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 27:97)A27 - 97
2X-RAY DIFFRACTION2(CHAIN A AND RESID 98:333)A98 - 333
3X-RAY DIFFRACTION3(CHAIN A AND RESID 334:576)A334 - 576
4X-RAY DIFFRACTION4(CHAIN B AND RESID 27:97)B27 - 97
5X-RAY DIFFRACTION5(CHAIN B AND RESID 98:333)B98 - 333
6X-RAY DIFFRACTION6(CHAIN B AND RESID 334:575)B334 - 575

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