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- PDB-28li: Crystal structure of complement-inhibiting protein ChiA of Borrel... -

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Basic information

Entry
Database: PDB / ID: 28li
TitleCrystal structure of complement-inhibiting protein ChiA of Borrelia recurrentis
ComponentsUncharacterized conserved protein
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. / Uncharacterized conserved protein
Function and homology information
Biological speciesBorrelia recurrentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized conserved protein
B: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4834
Polymers59,4342
Non-polymers492
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area24370 Å2
Unit cell
Length a, b, c (Å)53.070, 115.840, 83.030
Angle α, β, γ (deg.)90.000, 90.032, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21B-301-

MG

31A-404-

HOH

41B-405-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 29 through 213 or resid 222 through 265))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPILEILEAA29 - 26529 - 265
d_21ASPASPSERSERBB29 - 21329 - 213
d_22HISHISILEILEBB222 - 265222 - 265

NCS oper: (Code: givenMatrix: (0.99999962404, -0.000642165402709, -0.000582703397807), (-0.000641844170116, -0.999999642052, 0.000551299408518), (-0.000583057214637, -0.000550925196472, -0. ...NCS oper: (Code: given
Matrix: (0.99999962404, -0.000642165402709, -0.000582703397807), (-0.000641844170116, -0.999999642052, 0.000551299408518), (-0.000583057214637, -0.000550925196472, -0.999999678263)
Vector: -0.0297531923001, -23.2974843615, -41.5204698009)

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Components

#1: Protein Uncharacterized conserved protein


Mass: 29716.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia recurrentis (bacteria) / Gene: BDU_1021 / Production host: Escherichia coli (E. coli) / References: UniProt: B5RN86
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: sead bead method. Initial crystals sitting drop, 20% PEG400, 16% PEG4000, 70mM MgCl, 100mM Tris8.5 seed crystals hangig drop, 20%PEG400, 16%PEG4000, 50mM MgCl, 100mM Tris8.5
Temp details: initial crystal at 277 seed crystals 297

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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: May 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→48.25 Å / Num. obs: 13514 / % possible obs: 98.28 % / Redundancy: 6.5 % / Biso Wilson estimate: 63.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.47
Reflection shellResolution: 2.71→2.807 Å / Num. unique obs: 1343 / CC1/2: 0.782 / % possible all: 95.77

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→48.25 Å / SU ML: 0.4128 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.1169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2992 1347 9.99 %
Rwork0.2533 12135 -
obs0.2578 13482 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.76 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 2 15 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423699
X-RAY DIFFRACTIONf_angle_d0.96234992
X-RAY DIFFRACTIONf_chiral_restr0.0486587
X-RAY DIFFRACTIONf_plane_restr0.0065634
X-RAY DIFFRACTIONf_dihedral_angle_d6.3778507
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.706662284446 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.80.3881290.3391167X-RAY DIFFRACTION94.74
2.8-2.920.38341350.31161223X-RAY DIFFRACTION97.63
2.92-3.050.36671320.32061189X-RAY DIFFRACTION98
3.05-3.210.37181340.27891206X-RAY DIFFRACTION98.46
3.21-3.410.39641360.26091223X-RAY DIFFRACTION98.84
3.41-3.670.32161340.26771206X-RAY DIFFRACTION98.89
3.67-4.040.29321370.24531223X-RAY DIFFRACTION98.91
4.04-4.630.25681350.22251218X-RAY DIFFRACTION98.69
4.63-5.830.26681360.24821248X-RAY DIFFRACTION99.07
5.83-48.250.26211390.23481232X-RAY DIFFRACTION98.78

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