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- PDB-3r15: Structure Treponema Denticola Factor H Binding Protein -

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Basic information

Entry
Database: PDB / ID: 3r15
TitleStructure Treponema Denticola Factor H Binding Protein
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 / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsMiller, D.P. / McDowell, J.V. / Burgner, J. / Heroux, A. / Bell, J.K. / Marconi, R.T.
Citation
Journal: To be Published
Title: Structure Treponema Denticola Factor H Binding Protein
Authors: Miller, D.P. / McDowell, J.V. / Burgner, J. / Heroux, A. / Bell, J.K. / Marconi, R.T.
#1: Journal: To be Published
Title: Crystallization of the Factor H binding protein, FhbB, of 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 a unique interaction between the complement regulatory protein factor H and the periodontal pathogen Treponema denticola
Authors: McDowell, J.V. / Huang, B. / Fenno, J.C. / Marconi, R.T.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Factor H binding protein
B: Factor H binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2374
Polymers21,1202
Non-polymers1162
Water2,108117
1
A: Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)10,5601
Polymers10,5601
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)10,6763
Polymers10,5601
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.988, 46.988, 168.948
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-1-

SCN

31B-103-

SCN

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Components

#1: Protein Factor H binding protein


Mass: 10560.178 Da / Num. of mol.: 2 / Fragment: residues 24-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Strain: ATCC 35405 / Gene: fhbB, TDE_0108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73RI0
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.2 M sodium citrate tribasic dihydrate, 0.2 M sodium thiocyanate, 2.5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.5 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2010
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 39634 / Num. obs: 39492 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 %

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZ0

3qz0


Resolution: 1.701→36.079 Å / SU ML: 0.19 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 2122 10.16 %Random
Rwork0.2101 ---
obs0.2128 20883 95.74 %-
all-21812 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.074 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3186 Å2-0 Å2-0 Å2
2--0.3186 Å20 Å2
3----0.6373 Å2
Refinement stepCycle: LAST / Resolution: 1.701→36.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 6 117 1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071244
X-RAY DIFFRACTIONf_angle_d0.9841668
X-RAY DIFFRACTIONf_dihedral_angle_d12.428476
X-RAY DIFFRACTIONf_chiral_restr0.066194
X-RAY DIFFRACTIONf_plane_restr0.004210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7005-1.76130.23811750.20211700X-RAY DIFFRACTION88
1.7613-1.83180.23441910.18731773X-RAY DIFFRACTION93
1.8318-1.91520.20762150.20051811X-RAY DIFFRACTION95
1.9152-2.01620.2481950.20211846X-RAY DIFFRACTION96
2.0162-2.14250.2282300.19321870X-RAY DIFFRACTION97
2.1425-2.30790.22332320.19751820X-RAY DIFFRACTION97
2.3079-2.54010.24342240.20991904X-RAY DIFFRACTION97
2.5401-2.90750.28242220.23011933X-RAY DIFFRACTION98
2.9075-3.66260.24862100.21671994X-RAY DIFFRACTION98
3.6626-36.0870.20682280.20432110X-RAY DIFFRACTION98

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