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

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Basic information

Entry
Database: PDB / ID: 6kwj
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: 1.94 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 7, 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
B: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)25,4161
Polymers25,4161
Non-polymers00
Water4,504250
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 area13430 Å2
Unit cell
Length a, b, c (Å)128.501, 32.734, 72.247
Angle α, β, γ (deg.)90.000, 100.280, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Outer surface protein A / OspA163


Mass: 25416.320 Da / Num. of mol.: 1
Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,K117G,F126G,N127G,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.: 250 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 26%PEG 400, 0.1M Imidozole, 16.1 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→19.9 Å / Num. obs: 22185 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 28.2
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 11.6 / Num. unique obs: 1123 / % possible all: 99.8

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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: 1.94→19.9 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4942
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 1123 5.06 %
Rwork0.2011 21062 -
obs0.2032 22185 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 250 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581749
X-RAY DIFFRACTIONf_angle_d0.78112358
X-RAY DIFFRACTIONf_chiral_restr0.0539300
X-RAY DIFFRACTIONf_plane_restr0.0039295
X-RAY DIFFRACTIONf_dihedral_angle_d20.3526645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.030.31211430.25442595X-RAY DIFFRACTION99.49
2.03-2.140.30731490.232588X-RAY DIFFRACTION99.24
2.14-2.270.29761490.22492584X-RAY DIFFRACTION99.27
2.27-2.440.3121440.22822631X-RAY DIFFRACTION99.5
2.44-2.690.29061380.22972618X-RAY DIFFRACTION99.21
2.69-3.080.25491330.22472643X-RAY DIFFRACTION99.46
3.08-3.870.21131320.18562660X-RAY DIFFRACTION98.87
3.87-19.90.19441350.16752743X-RAY DIFFRACTION98.93

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