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- PDB-6j5m: OspA mutant, PSAM-VLGDV1-form3, grafted short chameleon sequence ... -

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Basic information

Entry
Database: PDB / ID: 6j5m
TitleOspA mutant, PSAM-VLGDV1-form3, grafted short chameleon sequence from alpha-B crystallin
ComponentsOuter surface protein A
KeywordsLIPID BINDING PROTEIN / Peptide Self-Assembly Mimic / single-layer beta-sheet / chameleon sequence
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 / Outer surface protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFujiwara, H. / Makabe, K.
CitationJournal: J Mol Liq / Year: 2019
Title: Beta-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals
Authors: Fujiwara, H. / Hongo, K. / Hori, Y. / Yoshida, N. / Makabe, K.
History
DepositionJan 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: 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 / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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


Theoretical massNumber of molelcules
Total (without water)26,3461
Polymers26,3461
Non-polymers00
Water4,125229
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 area13390 Å2
Unit cell
Length a, b, c (Å)33.142, 53.946, 65.937
Angle α, β, γ (deg.)90.00, 100.03, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45040, UniProt: P0CL66*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tri-HCl pH 8.5, 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 19236 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 24.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.84 / Num. unique obs: 935 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2A

5b2a


Resolution: 1.85→19.763 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 907 4.73 %RANDOM
Rwork0.1941 ---
obs0.1965 19186 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 229 2036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061821
X-RAY DIFFRACTIONf_angle_d0.7572457
X-RAY DIFFRACTIONf_dihedral_angle_d2.5821546
X-RAY DIFFRACTIONf_chiral_restr0.054314
X-RAY DIFFRACTIONf_plane_restr0.003306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.96580.27281590.23342964X-RAY DIFFRACTION96
1.9658-2.11750.2581360.20333012X-RAY DIFFRACTION97
2.1175-2.33020.26911420.19313032X-RAY DIFFRACTION97
2.3302-2.66670.29271510.21243052X-RAY DIFFRACTION98
2.6667-3.35710.25011590.20123090X-RAY DIFFRACTION99
3.3571-19.76440.21521600.17613129X-RAY DIFFRACTION99

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