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- PDB-7bml: Crystal structure of outer surface protein C (OspC) from Borrelia... -

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Basic information

Entry
Database: PDB / ID: 7bml
TitleCrystal structure of outer surface protein C (OspC) from Borrelia burgdorferi
ComponentsOuter surface protein C
KeywordsUNKNOWN FUNCTION / Lyme disease / tick-borne disease / OspC / Borrelia burgdorferi
Function / homologyLipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / cell outer membrane / Outer surface protein C
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSliwiak, J. / Bierwagen, P. / Ruszkowski, M. / Jaskolski, M. / Urbanowicz, A.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2015/17/B/NZ1/ 00873 Poland
Citation
Journal: To Be Published
Title: Structural studies of outer surface proteins (OspC) from different Borrelia strains
Authors: Sliwiak, J. / Bierwagen, P. / Ruszkowski, M. / Jaskolski, M. / Urbanowicz, A.
#1: Journal: FEBS J / Year: 2019
Title: Borrelia outer surface protein C is capable of human fibrinogen binding.
Authors: Bierwagen, P. / Szpotkowski, K. / Jaskolski, M. / Urbanowicz, A.
#2: Journal: Ticks Tick Borne Dis / Year: 2020
Title: Strong interactions between Salp15 homologues from the tick I. ricinus and distinct types of the outer surface OspC protein from Borrelia.
Authors: Bierwagen, P. / Sliwiak, J. / Jaskolski, M. / Urbanowicz, A.
#3: Journal: FEBS J / Year: 2019
Title: Borrelia outer surface protein C is capable of human fibrinogen binding.
Authors: Bierwagen, P. / Szpotkowski, K. / Jaskolski, M. / Urbanowicz, A.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer surface protein C
B: Outer surface protein C
C: Outer surface protein C
D: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)73,3524
Polymers73,3524
Non-polymers00
Water6,810378
1
A: Outer surface protein C
B: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)36,6762
Polymers36,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-36 kcal/mol
Surface area13640 Å2
MethodPISA
2
C: Outer surface protein C
D: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)36,6762
Polymers36,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-41 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.983, 48.769, 94.696
Angle α, β, γ (deg.)90.000, 96.190, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 6 or (resid 7...
21(chain B and (resid 5 through 6 or (resid 7...
31(chain C and (resid 5 through 6 or (resid 7...
41(chain D and (resid 5 through 8 or resid 11...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 6 or (resid 7...A5 - 6
121(chain A and (resid 5 through 6 or (resid 7...A7
131(chain A and (resid 5 through 6 or (resid 7...A4 - 164
141(chain A and (resid 5 through 6 or (resid 7...A4 - 164
211(chain B and (resid 5 through 6 or (resid 7...B5 - 6
221(chain B and (resid 5 through 6 or (resid 7...B7
231(chain B and (resid 5 through 6 or (resid 7...B5 - 160
241(chain B and (resid 5 through 6 or (resid 7...B5 - 160
251(chain B and (resid 5 through 6 or (resid 7...B5 - 160
261(chain B and (resid 5 through 6 or (resid 7...B5 - 160
271(chain B and (resid 5 through 6 or (resid 7...B5 - 160
311(chain C and (resid 5 through 6 or (resid 7...C5 - 6
321(chain C and (resid 5 through 6 or (resid 7...C7
331(chain C and (resid 5 through 6 or (resid 7...C5 - 163
341(chain C and (resid 5 through 6 or (resid 7...C5 - 163
411(chain D and (resid 5 through 8 or resid 11...D5 - 8
421(chain D and (resid 5 through 8 or resid 11...D11 - 64
431(chain D and (resid 5 through 8 or resid 11...D5 - 168
441(chain D and (resid 5 through 8 or resid 11...D14 - 160
451(chain D and (resid 5 through 8 or resid 11...D5 - 168
461(chain D and (resid 5 through 8 or resid 11...D5 - 168
471(chain D and (resid 5 through 8 or resid 11...D5 - 168
481(chain D and (resid 5 through 8 or resid 11...D5 - 168
491(chain D and (resid 5 through 8 or resid 11...D5 - 168

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Components

#1: Protein
Outer surface protein C / OspC from Borrelia burgdorferi


Mass: 18337.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: ospC / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q44977
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 1.69 Å3/Da / Density % sol: 27.38 % / Description: plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→53.67 Å / Num. obs: 45606 / % possible obs: 99.8 % / Redundancy: 6.581 % / Biso Wilson estimate: 31.099 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.158 / Χ2: 1.23 / Net I/σ(I): 8.82 / Num. measured all: 300133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.916.3851.3531.2246498732872820.6441.47599.4
1.91-2.046.8130.7942.2446918689468870.880.8699.9
2.04-2.26.6490.4913.7342880645864490.9440.53399.9
2.2-2.416.5440.3056.0238679591759110.9720.33299.9
2.41-2.76.860.2318.0837032540053980.9860.251100
2.7-3.126.50.13812.2730711473247250.9940.15199.9
3.12-3.816.6750.07921.2526940404440360.9970.08599.8
3.81-5.396.2340.05825.7319600316231440.9980.06399.4
5.39-53.676.130.04228.1110875178517740.9990.04699.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GGQ

1ggq


Resolution: 1.85→53.67 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1047 2.5 %
Rwork0.1896 40853 -
obs0.1912 41900 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.23 Å2 / Biso mean: 28.2566 Å2 / Biso min: 10.97 Å2
Refinement stepCycle: final / Resolution: 1.85→53.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 0 379 5087
Biso mean---31.36 -
Num. residues----640
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2770X-RAY DIFFRACTION10.68TORSIONAL
12B2770X-RAY DIFFRACTION10.68TORSIONAL
13C2770X-RAY DIFFRACTION10.68TORSIONAL
14D2770X-RAY DIFFRACTION10.68TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.950.35631470.28215705585298
1.95-2.070.35241490.241158175966100
2.07-2.230.2861480.216258145962100
2.23-2.450.25981490.193158385987100
2.45-2.810.28581490.196658455994100
2.81-3.540.23631510.172458506001100
3.54-53.670.19751540.16195984613899

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