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- PDB-8s2p: Crystal structure of Borrelia burgdorferi paralogous family 12 ou... -

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Basic information

Entry
Database: PDB / ID: 8s2p
TitleCrystal structure of Borrelia burgdorferi paralogous family 12 outer surface protein BBH37 (space group p21)
ComponentsLipoprotein, putative
KeywordsDNA BINDING PROTEIN / paralogous protein / PFam12
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein, putative
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrangulis, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2021/1-0068 Latvia
CitationJournal: To Be Published
Title: Crystal structure of Borrelia burgdorferi outer surface protein BBH37
Authors: Brangulis, K.
History
DepositionFeb 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lipoprotein, putative
BBB: Lipoprotein, putative


Theoretical massNumber of molelcules
Total (without water)45,2982
Polymers45,2982
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-15 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.090, 75.570, 113.160
Angle α, β, γ (deg.)90.000, 89.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipoprotein, putative


Mass: 22648.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first 4 residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_H37 / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50692
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.01 M MnCl2 0.1 M sodium citrate pH 5.6 2.5 M 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→62.924 Å / Num. obs: 18923 / % possible obs: 73.5 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.4
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2791 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→62.924 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: FREE R-VALUE / ESU R: 0.444 / ESU R Free: 0.316
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3096 946 5.001 %
Rwork0.2478 17971 -
all0.251 --
obs-18917 73.123 %
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: 34.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.009 Å2-0 Å2-0.022 Å2
2---0.006 Å2-0 Å2
3---0.015 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 26 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133037
X-RAY DIFFRACTIONr_bond_other_d0.0340.0163023
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6414047
X-RAY DIFFRACTIONr_angle_other_deg2.2891.5977000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56423.873173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.71415652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0181520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023400
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02660
X-RAY DIFFRACTIONr_nbd_refined0.2250.2748
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2270.22757
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21459
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.224
X-RAY DIFFRACTIONr_nbd_other0.2680.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1660.23
X-RAY DIFFRACTIONr_mcbond_it2.8573.3911494
X-RAY DIFFRACTIONr_mcbond_other2.8533.391493
X-RAY DIFFRACTIONr_mcangle_it4.0475.0711864
X-RAY DIFFRACTIONr_mcangle_other4.0475.0731865
X-RAY DIFFRACTIONr_scbond_it3.6063.8911543
X-RAY DIFFRACTIONr_scbond_other3.6033.8911543
X-RAY DIFFRACTIONr_scangle_it5.4225.6512183
X-RAY DIFFRACTIONr_scangle_other5.4225.6522184
X-RAY DIFFRACTIONr_lrange_it7.02740.4543418
X-RAY DIFFRACTIONr_lrange_other7.02640.4653419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.302750.2731301X-RAY DIFFRACTION71.8538
2.257-2.3190.3670.2751347X-RAY DIFFRACTION75.7771
2.319-2.3860.36590.2611309X-RAY DIFFRACTION77.4193
2.386-2.460.33710.2421283X-RAY DIFFRACTION76.5837
2.46-2.540.289620.2481221X-RAY DIFFRACTION73.6933
2.54-2.6290.306650.2551125X-RAY DIFFRACTION73.8672
2.629-2.7290.309420.2371125X-RAY DIFFRACTION72.1707
2.729-2.840.341650.2371006X-RAY DIFFRACTION72.2672
2.84-2.9660.293620.2311021X-RAY DIFFRACTION73.1757
2.966-3.1110.365630.247962X-RAY DIFFRACTION73.9005
3.111-3.2790.285660.265923X-RAY DIFFRACTION73.806
3.279-3.4780.421420.279859X-RAY DIFFRACTION71.6216
3.478-3.7180.305240.268812X-RAY DIFFRACTION69.3201
3.718-4.0150.285350.224781X-RAY DIFFRACTION74.3847
4.015-4.3980.265340.22737X-RAY DIFFRACTION74.206
4.398-4.9160.284340.237623X-RAY DIFFRACTION71.1809
4.916-5.6750.27310.294501X-RAY DIFFRACTION65.598
5.675-6.9450.383200.264481X-RAY DIFFRACTION72.2944
6.945-9.8040.181170.169366X-RAY DIFFRACTION68.1495
9.804-62.9240.52120.274188X-RAY DIFFRACTION65.3595

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