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

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Basic information

Entry
Database: PDB / ID: 6kwu
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: 1.43 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)25,7651
Polymers25,7651
Non-polymers00
Water6,503361
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 area13350 Å2
Unit cell
Length a, b, c (Å)33.081, 54.388, 66.236
Angle α, β, γ (deg.)90.000, 100.181, 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 / OspA149


Mass: 25764.631 Da / Num. of mol.: 1
Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,K117G,D118G,E128S,K129S,E131G,V132S,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.: 361 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 36% PEG 400, 0.1M Tris pH 7.0, 0.05M MgSO4, 24.6 mg/mL (12.3 mg/mL 2uL:1uL)

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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: 1.43→50 Å / Num. obs: 42482 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 20.2
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 7.27 / Num. unique obs: 2139 / % 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: 1.43→19.76 Å / SU ML: 0.1373 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.566
RfactorNum. reflection% reflection
Rfree0.217 2139 5.04 %
Rwork0.1849 --
obs0.1866 42481 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.97 Å2
Refinement stepCycle: LAST / Resolution: 1.43→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 361 2143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441795
X-RAY DIFFRACTIONf_angle_d0.72622420
X-RAY DIFFRACTIONf_chiral_restr0.0772308
X-RAY DIFFRACTIONf_plane_restr0.0032302
X-RAY DIFFRACTIONf_dihedral_angle_d3.31631075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.460.27551340.23632632X-RAY DIFFRACTION99.03
1.46-1.50.2251330.21732714X-RAY DIFFRACTION99.58
1.5-1.540.21481460.20382639X-RAY DIFFRACTION98.86
1.54-1.590.23131360.19662707X-RAY DIFFRACTION99.23
1.59-1.640.24571600.19662648X-RAY DIFFRACTION98.94
1.64-1.70.22361520.19212649X-RAY DIFFRACTION99.47
1.7-1.760.22081450.19072675X-RAY DIFFRACTION99.09
1.76-1.840.24281350.18262710X-RAY DIFFRACTION99.3
1.84-1.940.21621270.1852714X-RAY DIFFRACTION99.41
1.94-2.060.22151420.17922677X-RAY DIFFRACTION99.23
2.06-2.220.20891520.17492685X-RAY DIFFRACTION99.54
2.22-2.440.22091280.18542720X-RAY DIFFRACTION99.62
2.44-2.80.2061440.19652707X-RAY DIFFRACTION99.41
2.8-3.520.23281400.18552711X-RAY DIFFRACTION99.51
3.52-19.760.19821650.17182754X-RAY DIFFRACTION99.25

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