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- PDB-28lk: Crystal structure of complement-inhibiting protein ChiB of Borrel... -

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Basic information

Entry
Database: PDB / ID: 28lk
TitleCrystal structure of complement-inhibiting protein ChiB of Borrelia recurrentis
Componentscomplement-inhibiting protein ChiB
KeywordsPROTEIN BINDING / Borrelia recurrentis / louse-borne relapsing fever / surface protein / complement targeting and host interacting protein / complement-inhibiting protein
Function / homologyBorrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Chem-LPP / Uncharacterized conserved protein
Function and homology information
Biological speciesBorrelia recurrentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsFritz-Wolf, K. / Rahlfs, S. / Przyborski, J.M. / Stumpf, M. / Roettgerding, F. / Kraiczy, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUIDC3/E3 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Complement inhibition by a unique cluster of immunomodulatory outer surface proteins of Borrelia recurrentis.
Authors: Rottgerding, F. / Reyer, F. / Gerlach, E. / Amborn, M. / Duschek, N. / Schultze, T.G. / Fingerle, V. / Roome, C.M. / Stumpf, M. / Becker, K. / Rahlfs, S. / Przyborski, J.M. / Kraiczy, P. / Fritz-Wolf, K.
History
DepositionFeb 5, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: complement-inhibiting protein ChiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5545
Polymers31,6291
Non-polymers9254
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area14340 Å2
Unit cell
Length a, b, c (Å)82.010, 82.010, 90.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

21A-655-

HOH

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Components

#1: Protein complement-inhibiting protein ChiB


Mass: 31628.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia recurrentis (bacteria) / Gene: BDU_1020 / Production host: Escherichia coli (E. coli) / References: UniProt: B5RN85
#2: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.7 M Amoniumcitrat, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→36.68 Å / Num. obs: 49770 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 23.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.6
Reflection shellResolution: 1.501→1.555 Å / Num. unique obs: 4840 / CC1/2: 0.352

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→36.68 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 3982 8 %
Rwork0.1812 45788 -
obs0.1839 49770 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 62 263 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412139
X-RAY DIFFRACTIONf_angle_d1.20132867
X-RAY DIFFRACTIONf_chiral_restr0.0724311
X-RAY DIFFRACTIONf_plane_restr0.0102369
X-RAY DIFFRACTIONf_dihedral_angle_d9.6586320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.35851360.33081561X-RAY DIFFRACTION97.36
1.52-1.540.36321390.29811604X-RAY DIFFRACTION100
1.54-1.560.32081400.31613X-RAY DIFFRACTION100
1.56-1.580.30971410.29461621X-RAY DIFFRACTION100
1.58-1.60.29781400.27971606X-RAY DIFFRACTION100
1.6-1.630.29711400.27461614X-RAY DIFFRACTION99.94
1.63-1.650.29831420.26131629X-RAY DIFFRACTION100
1.65-1.680.30261400.24581603X-RAY DIFFRACTION100
1.68-1.710.27091410.24761626X-RAY DIFFRACTION100
1.71-1.740.32261390.23531601X-RAY DIFFRACTION100
1.74-1.770.27161420.22911627X-RAY DIFFRACTION100
1.77-1.810.26441400.23181613X-RAY DIFFRACTION100
1.81-1.850.32321400.24381617X-RAY DIFFRACTION100
1.85-1.890.23961420.23041629X-RAY DIFFRACTION100
1.89-1.940.25021400.19831615X-RAY DIFFRACTION99.83
1.94-1.990.23351420.1961629X-RAY DIFFRACTION100
1.99-2.050.23161420.19111634X-RAY DIFFRACTION100
2.05-2.120.22741410.17441620X-RAY DIFFRACTION100
2.12-2.190.22141420.17211634X-RAY DIFFRACTION100
2.19-2.280.19521440.1781651X-RAY DIFFRACTION100
2.28-2.380.18621420.17481638X-RAY DIFFRACTION100
2.38-2.510.22431410.17181623X-RAY DIFFRACTION99.32
2.51-2.670.1971450.16851664X-RAY DIFFRACTION99.83
2.67-2.870.19661430.17081646X-RAY DIFFRACTION100
2.87-3.160.23081470.171685X-RAY DIFFRACTION100
3.16-3.620.18171450.1561668X-RAY DIFFRACTION99.4
3.62-4.550.17561490.14251711X-RAY DIFFRACTION99.89
4.56-36.680.19571570.17931806X-RAY DIFFRACTION99.59

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