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- PDB-6kwv: A Crystal Structure of OspA mutant -

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Basic information

Entry
Database: PDB / ID: 6kwv
TitleA Crystal Structure of OspA mutant
ComponentsOuter surface protein A
KeywordsLIPID BINDING PROTEIN / Outer surface protein A / OspA
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein A
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKiya, M. / Makabe, K.
CitationJournal: J.Mol.Biol. / Year: 2024
Title: beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking.
Authors: Kiya, M. / Shiga, S. / Ding, P. / Koide, S. / Makabe, K.
History
DepositionSep 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)25,8791
Polymers25,8791
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13610 Å2
Unit cell
Length a, b, c (Å)34.437, 53.348, 65.501
Angle α, β, γ (deg.)90.000, 98.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Outer surface protein A / OspA143


Mass: 25878.732 Da / Num. of mol.: 1
Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,S118N,K119G,F126S,N127S,E128N,K129G,G130S,K239S,E240S,K254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ospA, BB_A15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 46.46 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 38% PEG 400, 0.1M Tris pH 8.0, 15.4mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 48779 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.2
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 8.94 / Num. unique obs: 2469

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 1.37→18.43 Å / SU ML: 0.1338 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.862
RfactorNum. reflection% reflection
Rfree0.2093 2469 5.06 %
Rwork0.191 --
obs0.192 48779 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.64 Å2
Refinement stepCycle: LAST / Resolution: 1.37→18.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 380 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451814
X-RAY DIFFRACTIONf_angle_d0.79232447
X-RAY DIFFRACTIONf_chiral_restr0.0867311
X-RAY DIFFRACTIONf_plane_restr0.0038306
X-RAY DIFFRACTIONf_dihedral_angle_d2.8721088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.25341260.23122349X-RAY DIFFRACTION92.04
1.4-1.430.22061420.2252575X-RAY DIFFRACTION99.41
1.43-1.460.26191330.21462575X-RAY DIFFRACTION99.63
1.46-1.490.2131280.21072568X-RAY DIFFRACTION99.59
1.49-1.530.20571320.20932590X-RAY DIFFRACTION99.63
1.53-1.570.26421280.20012585X-RAY DIFFRACTION99.71
1.57-1.620.24241420.20112556X-RAY DIFFRACTION99.74
1.62-1.670.22251610.20182562X-RAY DIFFRACTION99.96
1.67-1.730.22051280.19772599X-RAY DIFFRACTION99.96
1.73-1.80.21561420.20222555X-RAY DIFFRACTION99.93
1.8-1.880.21811420.19792581X-RAY DIFFRACTION99.89
1.88-1.980.22791330.18212599X-RAY DIFFRACTION99.82
1.98-2.10.19871380.17552583X-RAY DIFFRACTION99.85
2.1-2.260.19391370.18912596X-RAY DIFFRACTION99.82
2.26-2.490.22591300.20172604X-RAY DIFFRACTION99.85
2.49-2.850.25251350.20292602X-RAY DIFFRACTION99.85
2.85-3.590.18661340.18372603X-RAY DIFFRACTION99.64
3.59-18.430.18151580.17372628X-RAY DIFFRACTION98.79

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