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- PDB-8ec3: The crystal structure of the complement inhibitory domain of Borr... -

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Basic information

Entry
Database: PDB / ID: 8ec3
TitleThe crystal structure of the complement inhibitory domain of Borrelia hermsii FbpC.
ComponentsFibronectin-binding protein
KeywordsIMMUNE SYSTEM / Borrelia hermsii / complement / inhibitor
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Fibronectin-binding protein
Function and homology information
Biological speciesBorrelia hermsii HS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBooth, C.E. / Garcia, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146930 United States
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: Conformational dynamics of complement protease C1r inhibitor proteins from Lyme disease- and relapsing fever-causing spirochetes.
Authors: Roy, S. / Booth Jr., C.E. / Powell-Pierce, A.D. / Schulz, A.M. / Skare, J.T. / Garcia, B.L.
#1: Journal: Biorxiv / Year: 2023
Title: "Conformational dynamics of C1r inhibitor proteins from Lyme disease and relapsing fever spirochetes".
Authors: Roy, S. / Booth, C.E. / Powell-Pierce, A.D. / Schulz, A.M. / Skare, J.T. / Garcia, B.L.
History
DepositionSep 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9062
Polymers18,8811
Non-polymers241
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.239, 46.557, 45.186
Angle α, β, γ (deg.)90.000, 110.798, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fibronectin-binding protein


Mass: 18881.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia hermsii HS1 (bacteria) / Gene: cihC, A0V01_04335, BHA007 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9BXS5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.2 % / Description: Large birefringent plates
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystals were grown in the following condition containing 0.2M magnesium (II) chloride, 0.1M bis-tris (pH 5.5), and 25% PEG 3,350. Crystals were cryoprotected in a buffer containing 0.2M ...Details: Crystals were grown in the following condition containing 0.2M magnesium (II) chloride, 0.1M bis-tris (pH 5.5), and 25% PEG 3,350. Crystals were cryoprotected in a buffer containing 0.2M magnesium (II) chloride, 0.1M sodium citrate (pH 5.4), 25% PEG 3,350, and 10% glycerol.

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→31.28 Å / Num. obs: 23546 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Net I/σ(I): 19.4
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2109 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.218 / Rrim(I) all: 0.509 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.5→31.28 Å / SU ML: 0.1587 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.9463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1998 1919 8.46 %
Rwork0.1772 20769 -
obs0.1792 22688 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.39 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 1 157 1387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011247
X-RAY DIFFRACTIONf_angle_d1.05271667
X-RAY DIFFRACTIONf_chiral_restr0.0532189
X-RAY DIFFRACTIONf_plane_restr0.0076212
X-RAY DIFFRACTIONf_dihedral_angle_d15.7231485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.26651060.26271148X-RAY DIFFRACTION74.07
1.54-1.580.28081170.24631310X-RAY DIFFRACTION85.14
1.58-1.630.23781430.22331418X-RAY DIFFRACTION91.39
1.63-1.680.23451230.21461472X-RAY DIFFRACTION94.32
1.68-1.740.25821260.19591478X-RAY DIFFRACTION95.48
1.74-1.810.26711480.19971509X-RAY DIFFRACTION96.56
1.81-1.890.25131460.19241500X-RAY DIFFRACTION97.45
1.89-1.990.23131360.18711537X-RAY DIFFRACTION98.47
1.99-2.110.21691510.17681541X-RAY DIFFRACTION99.71
2.12-2.280.21351360.1651560X-RAY DIFFRACTION99.71
2.28-2.510.17081530.16341564X-RAY DIFFRACTION99.94
2.51-2.870.18461410.17381558X-RAY DIFFRACTION100
2.87-3.610.17361430.16371581X-RAY DIFFRACTION100
3.62-31.280.19441500.17591593X-RAY DIFFRACTION98.98

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