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- PDB-7fdd: A Crystal structure of OspA mutant -

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Basic information

Entry
Database: PDB / ID: 7fdd
TitleA Crystal structure of OspA mutant
ComponentsOuter surface protein A
KeywordsLIPOPROTEIN / Outer surface protein A / LIPID BINDING PROTEIN
Function / homology
Function and homology information


cell outer membrane / cell surface / membrane
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel ...C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Outer surface protein A
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShiga, S. / 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
DepositionJul 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
A: Outer surface protein A
B: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4234
Polymers51,2112
Non-polymers2122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer (in crystal)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-4 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.691, 128.806, 65.777
Angle α, β, γ (deg.)90.000, 118.868, 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


Mass: 25605.525 Da / Num. of mol.: 2
Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, E104S, K107S, Deletion 117-119, insertion GG, Deletion 124-127, Deletion 130-133, insertion TTT, K239S, E240S, K254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: OspA, BB_A15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
Has ligand of interestN

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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: 4.76 Å3/Da / Density % sol: 74.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Protein (16.0 mg/mL) 36% Polyethylene glycol 400, 0.1 M Imidazole (pH7.0)

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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 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→19.49 Å / Num. obs: 19789 / % possible obs: 93.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 64.66 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5091 / % possible all: 84.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Coot0.8.9.2model building
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LJY

6ljy


Resolution: 2.9→19.49 Å / SU ML: 0.5099 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2997 966 4.88 %
Rwork0.2695 18811 -
obs0.271 19777 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 14 0 3522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173536
X-RAY DIFFRACTIONf_angle_d0.50914766
X-RAY DIFFRACTIONf_chiral_restr0.0422612
X-RAY DIFFRACTIONf_plane_restr0.0018592
X-RAY DIFFRACTIONf_dihedral_angle_d18.27361304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.43391420.39212393X-RAY DIFFRACTION84.95
3.05-3.240.46281230.37852586X-RAY DIFFRACTION89.67
3.24-3.490.3378990.33672689X-RAY DIFFRACTION91.89
3.49-3.840.35941720.29612697X-RAY DIFFRACTION94.84
3.84-4.390.29631320.2632809X-RAY DIFFRACTION96.58
4.39-5.510.25171390.22342783X-RAY DIFFRACTION96.85
5.51-19.490.23571590.22252854X-RAY DIFFRACTION98.27
Refinement TLS params.Method: refined / Origin x: 21.3249549898 Å / Origin y: 15.9062406374 Å / Origin z: 17.4095804677 Å
111213212223313233
T0.530764055674 Å20.019987399137 Å2-0.00801364897591 Å2-0.522964853775 Å20.0024285791834 Å2--0.42065578258 Å2
L0.540618029328 °20.0818162121154 °2-0.062620124827 °2-0.678489614654 °20.0766887573222 °2--0.214592198966 °2
S0.0263837060687 Å °0.00523081129348 Å °0.0551152820632 Å °-0.0593936207354 Å °-0.0561647146879 Å °-0.0735338297079 Å °0.0248894842298 Å °-0.045335420391 Å °0.0455803254474 Å °
Refinement TLS groupSelection details: all

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