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- PDB-6j49: Grafting VLADV sequence into OspAsm1 -

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Basic information

Entry
Database: PDB / ID: 6j49
TitleGrafting VLADV sequence into OspAsm1
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
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: 5B10
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

Downloads & links

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Assembly

Deposited unit
O: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7483
Polymers26,3601
Non-polymers3882
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint10 kcal/mol
Surface area13360 Å2
Unit cell
Length a, b, c (Å)33.229, 54.485, 66.489
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer surface protein A


Mass: 26359.568 Da / Num. of mol.: 1
Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,S120V,S121L,T122A,E123D,E124V,E196A,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 (E. coli) / References: UniProt: P0CL66
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 34% PEG 400, 0.1M Tris pH 8.8

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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 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 30305 / % possible obs: 97.83 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 25.9
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 1482 / % 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: 1.6→19.886 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.77
RfactorNum. reflection% reflection
Rfree0.2179 1529 5.05 %
Rwork0.1811 --
obs0.183 30286 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 26 276 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061877
X-RAY DIFFRACTIONf_angle_d0.8022527
X-RAY DIFFRACTIONf_dihedral_angle_d3.7381578
X-RAY DIFFRACTIONf_chiral_restr0.059318
X-RAY DIFFRACTIONf_plane_restr0.004314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6005-1.65210.3061440.24722548X-RAY DIFFRACTION96
1.6521-1.71110.26871260.22312542X-RAY DIFFRACTION97
1.7111-1.77960.23061370.1992576X-RAY DIFFRACTION97
1.7796-1.86050.22471300.18162603X-RAY DIFFRACTION97
1.8605-1.95850.21851470.18122597X-RAY DIFFRACTION98
1.9585-2.08110.2361380.17942602X-RAY DIFFRACTION98
2.0811-2.24160.18811200.17272636X-RAY DIFFRACTION98
2.2416-2.46680.22741470.18462633X-RAY DIFFRACTION99
2.4668-2.82290.21271220.19472654X-RAY DIFFRACTION99
2.8229-3.55320.23711680.18222649X-RAY DIFFRACTION99
3.5532-19.88750.18841500.16352717X-RAY DIFFRACTION100

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