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- PDB-6j47: OspA variant with a short chameleon sequence from alpha B crystallin -

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Basic information

Entry
Database: PDB / ID: 6j47
TitleOspA variant with a short chameleon sequence from alpha B crystallin
ComponentsOuter surface protein A
KeywordsLIPID BINDING PROTEIN / beta-sheet / DE NOVO 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
Outer surface protein A / Outer surface protein A
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMakabe, K. / Hori, Y.
CitationJournal: Proteins / Year: 2019
Title: Grafting a short chameleon sequence from alpha B crystallin into a beta-sheet scaffold protein.
Authors: Hori, Y. / Fujiwara, H. / Fujiwara, W. / Makabe, K.
History
DepositionJan 8, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 6, 2019ID: 5B3M
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8564
Polymers26,3461
Non-polymers5113
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint18 kcal/mol
Surface area13100 Å2
Unit cell
Length a, b, c (Å)33.204, 53.173, 64.271
Angle α, β, γ (deg.)90.00, 99.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer surface protein A


Mass: 26345.543 Da / Num. of mol.: 1
Mutation: E37S, E45S, K46S,K64S, E104S, K107S, K239S, E240S, K254S, K48A, K60A, K83A, E196A, S120V,S121L, T122G, E123D, E124V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: ospA / Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 40% PEG 400, 0.1M Tris-HCl pH 9.0, protein 10 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: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→63.32 Å / Num. obs: 17284 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.72 / Num. unique obs: 833 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 1.9→27.002 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.81
RfactorNum. reflection% reflection
Rfree0.263 873 5.06 %
Rwork0.2143 --
obs0.2168 17249 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 34 64 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061856
X-RAY DIFFRACTIONf_angle_d0.9132493
X-RAY DIFFRACTIONf_dihedral_angle_d4.0331563
X-RAY DIFFRACTIONf_chiral_restr0.058313
X-RAY DIFFRACTIONf_plane_restr0.005308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8973-2.01610.31091480.24362641X-RAY DIFFRACTION97
2.0161-2.17170.26011350.22242731X-RAY DIFFRACTION98
2.1717-2.39020.28971470.19652745X-RAY DIFFRACTION99
2.3902-2.73580.27581480.20582732X-RAY DIFFRACTION99
2.7358-3.44560.26971410.22332785X-RAY DIFFRACTION100
3.4456-27.00430.24781540.21132742X-RAY DIFFRACTION97

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