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

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Basic information

Entry
Database: PDB / ID: 7nen
TitleCrystal structure of outer surface protein C (OspC) from Borrelia garinii
ComponentsOuter surface protein C
KeywordsUNKNOWN FUNCTION / Lyme disease / tick-borne disease / OspC / Borrelia garinii
Function / homologyLipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer surface protein C
Function and homology information
Biological speciesBorrelia garinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 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

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Assembly

Deposited unit
A: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)18,6491
Polymers18,6491
Non-polymers00
Water2,954164
1
A: Outer surface protein C

A: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)37,2992
Polymers37,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area3750 Å2
ΔGint-33 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.000, 151.850, 57.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

21A-332-

HOH

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Components

#1: Protein Outer surface protein C


Mass: 18649.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia garinii (bacteria) / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / References: UniProt: H6VGK2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium acetate trihydrate 25% w/v PEG 3350 0.1M sodium HEPES pH 7.5 protein 30 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.98→31.75 Å / Num. obs: 14012 / % possible obs: 96.1 % / Redundancy: 9.25 % / Biso Wilson estimate: 28.231 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.153 / Χ2: 0.845 / Net I/σ(I): 10.73 / Num. measured all: 129617 / Scaling rejects: 5392
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
1.98-2.038.4190.8981.888815105010470.930.95799.7
2.03-2.097.7070.5984.068046104510440.7950.64299.9
2.09-2.159.8090.5393.519809100210000.950.5799.8
2.15-2.2110.2750.6583.0383849558160.9580.69385.4
2.21-2.297.5760.27711.4763499608380.9530.29787.3
2.29-2.379.220.514.0160859156600.9820.5472.1
2.37-2.4610.280.2316.8392429008990.9960.24399.9
2.46-2.5610.2320.2078.4787698578570.9920.218100
2.56-2.6710.0410.2038.8981338108100.9920.214100
2.67-2.810.0520.16610.3978617827820.9950.175100
2.8-2.9510.1130.14510.977167637630.9950.152100
2.95-3.139.9990.11913.9370797087080.9970.126100
3.13-3.359.9110.10315.5766706736730.9980.109100
3.35-3.629.1290.10618.1357976376350.9960.11299.7
3.62-3.967.970.11321.3945515815710.9930.12198.3
3.96-4.439.1670.07722.7247305345160.9980.08196.6
4.43-5.118.9790.06523.6842024714680.9980.06999.4
5.11-6.268.8630.05823.1836164084080.9980.062100
6.26-8.857.8440.04523.7425653283270.9990.04799.7
8.85-31.756.3050.03925.1911981971900.9990.04296.4

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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: 7BML

7bml


Resolution: 1.98→31.75 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.328 1045 7.48 %
Rwork0.2551 12928 -
obs0.2604 13973 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.43 Å2 / Biso mean: 34.7542 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 1.98→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 0 168 1307
Biso mean---32.8 -
Num. residues----160
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 (%)
1.98-2.080.41731500.34821873202399
2.08-2.210.42071400.32691740188093
2.22-2.390.56291280.41791567169582
2.39-2.630.281530.257518962049100
2.63-3.010.31131550.236319102065100
3.01-3.790.29041580.202819412099100
3.79-31.750.25141610.20262001216298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.96040.9374-0.14691.3138-0.27810.67180.1864-0.08441.2883-0.13290.15020.1527-0.39310.0838-0.04620.2245-0.00480.10640.40230.07580.462719.125255.648443.8877
23.20131.18640.49161.1534-0.31591.20150.1930.0504-0.04670.0864-0.11790.2477-0.0494-0.1084-0.11710.0936-0.0224-0.01230.36850.02850.093113.634137.5943.5536
31.412-0.4076-0.70280.38330.61640.9933-0.2980.36711.1017-0.51990.24040.1576-0.6327-0.0190.15450.41170.0366-0.14670.40320.18860.564410.834155.92139.3959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 37 )A5 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 135 )A38 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 164 )A136 - 164

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