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

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Basic information

Entry
Database: PDB / ID: 6ljy
TitleA Crystal Structure of OspA mutant
ComponentsOspA163
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 speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 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

Downloads & links

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Assembly

Deposited unit
O: OspA163


Theoretical massNumber of molelcules
Total (without water)25,4161
Polymers25,4161
Non-polymers00
Water6,467359
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 area13180 Å2
Unit cell
Length a, b, c (Å)33.137, 54.560, 66.095
Angle α, β, γ (deg.)90.000, 99.768, 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 OspA163


Mass: 25416.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 38%PEG400, 0.1M Tris-HCl, 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: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→19.86 Å / Num. obs: 37055 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 14.16 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 22
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 8.2 / Num. unique obs: 1801 / % possible all: 99.2

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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: 1.5→19.86 Å / SU ML: 0.1345 / Cross valid method: FREE R-VALUE / Phase error: 20.023
RfactorNum. reflection% reflection
Rfree0.2109 1801 4.86 %
Rwork0.1699 --
obs0.1719 37055 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 359 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631852
X-RAY DIFFRACTIONf_angle_d0.82592532
X-RAY DIFFRACTIONf_chiral_restr0.0567329
X-RAY DIFFRACTIONf_plane_restr0.0041318
X-RAY DIFFRACTIONf_dihedral_angle_d2.35971921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.21871440.18512667X-RAY DIFFRACTION99.29
1.54-1.590.21251330.17862728X-RAY DIFFRACTION99.55
1.59-1.640.23471220.17112734X-RAY DIFFRACTION99.96
1.64-1.70.22061170.17952695X-RAY DIFFRACTION99.89
1.7-1.760.21931360.17962747X-RAY DIFFRACTION99.9
1.76-1.840.20011350.17032726X-RAY DIFFRACTION99.93
1.84-1.940.18841400.17432710X-RAY DIFFRACTION99.1
1.94-2.060.20451590.16322660X-RAY DIFFRACTION99.37
2.06-2.220.2181220.16612706X-RAY DIFFRACTION98.71
2.22-2.440.21591340.1742706X-RAY DIFFRACTION99.02
2.44-2.80.21221620.17462683X-RAY DIFFRACTION99.06
2.8-3.520.21021550.16712697X-RAY DIFFRACTION98.92
3.52-19.860.21061420.16432795X-RAY DIFFRACTION99.56

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