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- PDB-3qz0: Structure of Treponema denticola Factor H Binding protein (FhbB),... -

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Basic information

Entry
Database: PDB / ID: 3qz0
TitleStructure of Treponema denticola Factor H Binding protein (FhbB), selenomethionine derivative
ComponentsFactor H binding protein
KeywordsPROTEIN BINDING / Factor H binding protein / Factor H
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2300 / : / : / Factor H binding protein B / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
THIOCYANATE ION / Factor H binding protein B domain-containing protein
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsMiller, D.P. / McDowell, J.V. / Heroux, A. / Bell, J.K. / Marconi, R.T. / Conrad, D.H. / Burgner, J.W.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structure of factor H-binding protein B (FhbB) of the periopathogen, Treponema denticola: insights into progression of periodontal disease.
Authors: Miller, D.P. / Bell, J.K. / McDowell, J.V. / Conrad, D.H. / Burgner, J.W. / Heroux, A. / Marconi, R.T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization of the factor H-binding protein, FhbB, from the periopathogen Treponema denticola.
Authors: Miller, D.P. / McDowell, J.V. / Bell, J.K. / Marconi, R.T.
#2: Journal: Infect.Immun. / Year: 2009
Title: Analysis of unique interaction between complement regulatory protein factor H and periodontal pathogen Treponema denticola
Authors: McDowell, J.V. / Huang, B. / Fenno, J.C. / Marconi, R.T.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Structure summary
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Jun 20, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Factor H binding protein
B: Factor H binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6105
Polymers21,4022
Non-polymers2083
Water2,738152
1
A: Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)10,7011
Polymers10,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Factor H binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9094
Polymers10,7011
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.921, 46.921, 168.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1-

SCN

21B-103-

SCN

31B-103-

SCN

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Components

#1: Protein Factor H binding protein


Mass: 10700.863 Da / Num. of mol.: 2 / Fragment: residues 24-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Strain: 35405 / Gene: fhbB, TDE_0108 / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)(pLyS) / References: UniProt: Q73RI0
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.39 M sodium citrate, 0.1 M HEPES, 0.2 M sodium thiocyanate, 10 mM dithiothreitol, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2822 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 19293 / Num. obs: 19167 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEwithin PHENIXphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.77→45.207 Å / SU ML: 0.18 / σ(F): 0.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1903 10 %RANDOM
Rwork0.1889 ---
obs0.1906 19030 98.35 %-
all-19293 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.98 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6285 Å2-0 Å20 Å2
2---0.6285 Å2-0 Å2
3---1.257 Å2
Refinement stepCycle: LAST / Resolution: 1.77→45.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 12 152 1395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061284
X-RAY DIFFRACTIONf_angle_d1.0381725
X-RAY DIFFRACTIONf_dihedral_angle_d13.066500
X-RAY DIFFRACTIONf_chiral_restr0.07200
X-RAY DIFFRACTIONf_plane_restr0.004216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7704-1.83370.2461830.19331648X-RAY DIFFRACTION97
1.8337-1.90710.24041830.18661646X-RAY DIFFRACTION97
1.9071-1.99390.21971830.19091652X-RAY DIFFRACTION98
1.9939-2.09910.19551870.17841675X-RAY DIFFRACTION99
2.0991-2.23060.18181910.17651715X-RAY DIFFRACTION99
2.2306-2.40280.23681870.18071689X-RAY DIFFRACTION99
2.4028-2.64460.21981920.19451729X-RAY DIFFRACTION99
2.6446-3.02720.19131930.20361740X-RAY DIFFRACTION99
3.0272-3.81360.1971960.18891761X-RAY DIFFRACTION99
3.8136-45.22170.19032080.18131872X-RAY DIFFRACTION97

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