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- PDB-6fzz: Crystal structure of BSE31 (BSPA14S_RS05060 gene product) from Ly... -

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Basic information

Entry
Database: PDB / ID: 6fzz
TitleCrystal structure of BSE31 (BSPA14S_RS05060 gene product) from Lyme disease agent Borrelia (Borreliella) spielmanii
ComponentsVirulent strain associated lipoprotein
KeywordsPROTEIN BINDING / Outer surface protein / borrelia outer membrane / pFam54 family
Function / homologyBorrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Virulent strain associated lipoprotein
Function and homology information
Biological speciesBorreliella spielmanii A14S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBrangulis, K. / Akopjana, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
ERDF/CFCA/SEDA1.1.1.2/VIAA/1/16/144 Latvia
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: BBE31 from the Lyme disease agent Borrelia burgdorferi, known to play an important role in successful colonization of the mammalian host, shows the ability to bind glutathione.
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Zelencova, D. / Jekabsons, A. / Jaudzems, K. / Tars, K.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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: Virulent strain associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9075
Polymers25,1301
Non-polymers7774
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint23 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.140, 64.140, 97.371
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Virulent strain associated lipoprotein


Mass: 25129.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first four residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borreliella spielmanii A14S (bacteria) / Gene: BSPA14S_J0028 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C0RBM0
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Sodium citrate 0.1 M Tris pH 8.5 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→55.55 Å / Num. obs: 15078 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.8
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1279 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FXE

6fxe


Resolution: 2.05→55.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.851 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 760 5.1 %RANDOM
Rwork0.186 ---
obs0.1888 14287 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83 Å2 / Biso mean: 32.4 Å2 / Biso min: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.05→55.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 52 54 1754
Biso mean--48.02 40.57 -
Num. residues----199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191715
X-RAY DIFFRACTIONr_bond_other_d0.0020.021752
X-RAY DIFFRACTIONr_angle_refined_deg1.8382.0132275
X-RAY DIFFRACTIONr_angle_other_deg0.93534070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8515198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81826.34182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57515367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.786157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 56 -
Rwork0.15 1014 -
all-1070 -
obs--100 %

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