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- PDB-6hpn: Crystal structure of Borrelia spielmanii WP_012665240 (BSA64) - a... -

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Basic information

Entry
Database: PDB / ID: 6hpn
TitleCrystal structure of Borrelia spielmanii WP_012665240 (BSA64) - an orthologous protein to B. burgdorferi BBA64
ComponentsAntigen, P35
KeywordsMEMBRANE PROTEIN / Outer surface protein / PFam54.
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha / Antigen, P35
Function and homology information
Biological speciesBorreliella spielmanii A14S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsBrangulis, K. / Akopjana, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/1/16/144 Latvia
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural analysis of the outer surface proteins from Borrelia burgdorferi paralogous gene family 54 that are thought to be the key players in the pathogenesis of Lyme disease.
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
History
DepositionSep 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 29, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 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: Antigen, P35


Theoretical massNumber of molelcules
Total (without water)25,8761
Polymers25,8761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.442, 77.442, 104.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Antigen, P35


Mass: 25876.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are the remnants from the expression tag.
Source: (gene. exp.) Borreliella spielmanii A14S (bacteria) / Gene: BSPA14S_A0059 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0RC68

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1 M Sodium citrate 15% 2-propanol 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.25 Å / Num. obs: 10298 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 19
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9 / Num. unique obs: 1470 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ALY

4aly


Resolution: 2.6→43.25 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.987 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.429 / ESU R Free: 0.271
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 494 4.8 %RANDOM
Rwork0.2077 ---
obs0.2094 9764 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.08 Å2 / Biso mean: 24.556 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.6→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 0 0 1733
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131760
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171667
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6322374
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5813894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00625.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41915348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.299156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021919
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 37 -
Rwork0.244 713 -
all-750 -
obs--100 %

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