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- PDB-8q4k: Crystal structure of Borrelia burgdorferi BB0158 -

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Basic information

Entry
Database: PDB / ID: 8q4k
TitleCrystal structure of Borrelia burgdorferi BB0158
ComponentsS2 lipoprotein
KeywordsMEMBRANE PROTEIN / Lyme disease / outer surface protein / borreliosis.
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / S2 lipoprotein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrangulis, K. / Tars, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/20/A/048European Union
CitationJournal: Ticks Tick Borne Dis / Year: 2024
Title: Structural studies of chromosomally encoded outer surface lipoprotein BB0158 from Borrelia burgdorferi sensu stricto.
Authors: Brangulis, K. / Akopjana, I. / Bogans, J. / Kazaks, A. / Tars, K.
History
DepositionAug 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: S2 lipoprotein
BBB: S2 lipoprotein
CCC: S2 lipoprotein
DDD: S2 lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1237
Polymers96,8354
Non-polymers2883
Water4,468248
1
AAA: S2 lipoprotein
BBB: S2 lipoprotein
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 48.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)48,6094
Polymers48,4172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-77 kcal/mol
Surface area18870 Å2
2
CCC: S2 lipoprotein
DDD: S2 lipoprotein
hetero molecules


  • defined by author
  • 48.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)48,5133
Polymers48,4172
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-49 kcal/mol
Surface area18790 Å2
Unit cell
Length a, b, c (Å)75.063, 81.774, 80.801
Angle α, β, γ (deg.)90.000, 109.381, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
S2 lipoprotein


Mass: 24208.658 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0158 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51180
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate 0.1 M sodium acetate (pH 4.6) 20% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→44.97 Å / Num. obs: 35959 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4 / Num. unique obs: 3725 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.97 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.323
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2973 1821 5.066 %
Rwork0.213 34128 -
all0.217 --
obs-35949 99.255 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å20.004 Å2
2---0.003 Å2-0 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 15 248 6736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136603
X-RAY DIFFRACTIONr_bond_other_d0.0340.0166434
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6378897
X-RAY DIFFRACTIONr_angle_other_deg2.2871.58614959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93826.545275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.399151301
X-RAY DIFFRACTIONr_chiral_restr0.0650.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027196
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021308
X-RAY DIFFRACTIONr_nbd_refined0.210.21220
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.25933
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23076
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3430.218
X-RAY DIFFRACTIONr_nbd_other0.3030.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.25
X-RAY DIFFRACTIONr_mcbond_it4.1154.9793223
X-RAY DIFFRACTIONr_mcbond_other4.1134.9793222
X-RAY DIFFRACTIONr_mcangle_it6.0447.454020
X-RAY DIFFRACTIONr_mcangle_other6.0447.454021
X-RAY DIFFRACTIONr_scbond_it4.245.3713380
X-RAY DIFFRACTIONr_scbond_other4.2065.3633369
X-RAY DIFFRACTIONr_scangle_it6.4177.8784877
X-RAY DIFFRACTIONr_scangle_other6.4177.8664860
X-RAY DIFFRACTIONr_lrange_it9.11557.4897112
X-RAY DIFFRACTIONr_lrange_other9.10957.477099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3591430.2752511X-RAY DIFFRACTION99.6246
2.462-2.530.3461330.272415X-RAY DIFFRACTION98.2267
2.53-2.6030.2951210.2322402X-RAY DIFFRACTION99.3698
2.603-2.6830.361370.2622284X-RAY DIFFRACTION99.5068
2.683-2.7710.3951110.2682253X-RAY DIFFRACTION99.5788
2.771-2.8680.3761010.232193X-RAY DIFFRACTION99.2644
2.868-2.9760.3271050.2122086X-RAY DIFFRACTION99.6362
2.976-3.0970.3171040.222039X-RAY DIFFRACTION99.6744
3.097-3.2350.3161070.2241904X-RAY DIFFRACTION98.0976
3.235-3.3920.3181110.2281843X-RAY DIFFRACTION99.4402
3.392-3.5760.3191090.2371771X-RAY DIFFRACTION99.8407
3.576-3.7920.271810.2141667X-RAY DIFFRACTION99.6011
3.792-4.0530.244900.1791583X-RAY DIFFRACTION99.7615
4.053-4.3770.223730.1651458X-RAY DIFFRACTION99.5449
4.377-4.7930.241670.1641344X-RAY DIFFRACTION97.6471
4.793-5.3560.271640.1781236X-RAY DIFFRACTION99.3884
5.356-6.180.325670.2151067X-RAY DIFFRACTION99.561
6.18-7.5560.333350.239949X-RAY DIFFRACTION99.2936
7.556-10.6340.283330.179712X-RAY DIFFRACTION98.545
10.634-44.970.258290.254411X-RAY DIFFRACTION98.2143

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