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- PDB-8xwg: OspA variants for thioflavin-T binding -

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Basic information

Entry
Database: PDB / ID: 8xwg
TitleOspA variants for thioflavin-T binding
ComponentsOuter Surface Protein A
KeywordsUNKNOWN FUNCTION / beta-sheet / thioflavin-T / amyloid
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Outer Surface Protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMakabe, K. / Miura, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Science and Technology Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Redesign of a thioflavin-T-binding protein with a flat beta-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity.
Authors: Miura, Y. / Namioka, S. / Iwai, A. / Yoshida, N. / Konno, H. / Sohma, Y. / Kanai, M. / Makabe, K.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)34,4881
Polymers34,4881
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.183, 35.807, 92.397
Angle α, β, γ (deg.)90.000, 105.990, 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: 34488.406 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 (E. coli) / References: UniProt: D0VWU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 / Details: 42%(w/v) PEG400, 0.1 M Tris-HCl, 15 mg/mL protein

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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 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.66 Å / Num. obs: 22435 / % possible obs: 97.19 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.98
Reflection shellResolution: 2→2.071 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.6916 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1831 / CC1/2: 0.74 / % possible all: 80.48

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.66 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 1124 5.02 %
Rwork0.2321 21281 -
obs0.2345 22405 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.34 Å2
Refinement stepCycle: LAST / Resolution: 2→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 103 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692409
X-RAY DIFFRACTIONf_angle_d0.86453240
X-RAY DIFFRACTIONf_chiral_restr0.0488396
X-RAY DIFFRACTIONf_plane_restr0.0054405
X-RAY DIFFRACTIONf_dihedral_angle_d6.0725330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.35291040.30122219X-RAY DIFFRACTION82.41
2.09-2.20.29041240.282711X-RAY DIFFRACTION99.06
2.2-2.340.36761730.25852673X-RAY DIFFRACTION99.86
2.34-2.520.34951360.26962697X-RAY DIFFRACTION99.65
2.52-2.770.29131600.24982722X-RAY DIFFRACTION99.86
2.77-3.170.29061530.25052708X-RAY DIFFRACTION99.83
3.17-3.990.24911500.20552738X-RAY DIFFRACTION99.04
3.99-19.660.22581240.19252813X-RAY DIFFRACTION98.62

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