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- PDB-3hoe: Crystal Structure of Surface Lipoprotein -

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Basic information

Entry
Database: PDB / ID: 3hoe
TitleCrystal Structure of Surface Lipoprotein
ComponentsTbpB
KeywordsTRANSPORT PROTEIN / Iron acquisition / ion transport / receptor / transferrin / vaccine
Function / homology
Function and homology information


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 / 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 - #250 / 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 2
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.303 Å
AuthorsMoraes, T.F. / Yu, R.H. / Schryvers, A.B. / Strynadka, N.C.J.
CitationJournal: Mol.Cell / Year: 2009
Title: Insights into the bacterial transferrin receptor: the structure of transferrin-binding protein B from Actinobacillus pleuropneumoniae.
Authors: Moraes, T.F. / Yu, R.H. / Strynadka, N.C. / Schryvers, A.B.
History
DepositionJun 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TbpB
B: TbpB


Theoretical massNumber of molelcules
Total (without water)56,2042
Polymers56,2042
Non-polymers00
Water2,486138
1
A: TbpB


Theoretical massNumber of molelcules
Total (without water)28,1021
Polymers28,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TbpB


Theoretical massNumber of molelcules
Total (without water)28,1021
Polymers28,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.473, 43.431, 100.397
Angle α, β, γ (deg.)90.00, 118.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TbpB / Transferrin binding protein 2


Mass: 28101.988 Da / Num. of mol.: 2 / Fragment: residues 56-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Gene: tbpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q44124
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG3350, 0.1M Tris pH 8.0, 150 mM NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98057, 0.98088, 0.97007
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2008
Details: a double crystal monochromator (DCM) with an indirectly cryo-cooled first DCM w ith cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically f ocusing mirror.
RadiationMonochromator: a double crystal monochromator (DCM) with an indirectly cryo-cooled first DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980571
20.980881
30.970071
ReflectionResolution: 2.303→35.31 Å / Num. obs: 42372 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rsym value: 0.07 / Net I/σ(I): 29.6

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Processing

Software
NameVersionClassification
MacromolecularCrystallography Data Collection (MXDC) GUIdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.303→35.308 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 2185 5.16 %RANDOM
Rwork0.1944 ---
all0.1979 42372 --
obs0.1979 42372 90.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.634 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 96.66 Å2 / Biso mean: 45.479 Å2 / Biso min: 22.82 Å2
Baniso -1Baniso -2Baniso -3
1-3.798 Å20 Å2-3.968 Å2
2--12.128 Å20 Å2
3----15.926 Å2
Refinement stepCycle: LAST / Resolution: 2.303→35.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 0 138 3913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083858
X-RAY DIFFRACTIONf_angle_d1.1085204
X-RAY DIFFRACTIONf_dihedral_angle_d17.781380
X-RAY DIFFRACTIONf_chiral_restr0.073541
X-RAY DIFFRACTIONf_plane_restr0.004684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.303-2.35340.2655830.23631271X-RAY DIFFRACTION46.64
2.3534-2.40820.30631020.24271722X-RAY DIFFRACTION60.78
2.4082-2.46840.33111170.24321990X-RAY DIFFRACTION73.26
2.4684-2.53510.341280.25392359X-RAY DIFFRACTION84.19
2.5351-2.60970.29841240.25952562X-RAY DIFFRACTION91.83
2.6097-2.69390.34421360.26372688X-RAY DIFFRACTION95.7
2.6939-2.79010.34391130.25172745X-RAY DIFFRACTION98.69
2.7901-2.90180.33741710.22942761X-RAY DIFFRACTION98.95
2.9018-3.03380.32841680.23462700X-RAY DIFFRACTION98.73
3.0338-3.19360.27951320.20532714X-RAY DIFFRACTION98.17
3.1936-3.39360.22251170.20712848X-RAY DIFFRACTION99.33
3.3936-3.65530.25721470.1872773X-RAY DIFFRACTION99.76
3.6553-4.02270.25791950.16742734X-RAY DIFFRACTION99.9
4.0227-4.60370.16491680.14192743X-RAY DIFFRACTION99.66
4.6037-5.7960.21031430.13662783X-RAY DIFFRACTION99.86
5.796-35.31230.19341410.15042794X-RAY DIFFRACTION99.42

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