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- PDB-6j6e: Borrelia burgdorferi OspA via surface entropy reduction (form5) -

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Basic information

Entry
Database: PDB / ID: 6j6e
TitleBorrelia burgdorferi OspA via surface entropy reduction (form5)
ComponentsOuter surface protein A
KeywordsLIPID BINDING PROTEIN / single-layer beta-sheet
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
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 14, 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)26,3951
Polymers26,3951
Non-polymers00
Water7,242402
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 area13420 Å2
Unit cell
Length a, b, c (Å)32.974, 53.984, 66.120
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer surface protein A


Mass: 26395.469 Da / Num. of mol.: 1
Mutation: 37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,T122G,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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Imidazole pH 6.0, 38% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 36144 / % possible obs: 97.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 19.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 1754 / % possible all: 95.6

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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: 2G8C

2g8c


Resolution: 1.5→19.13 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.99
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 1801 5.06 %RANDOM
Rwork0.1752 ---
obs0.1758 35619 97.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 402 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061839
X-RAY DIFFRACTIONf_angle_d0.8512485
X-RAY DIFFRACTIONf_dihedral_angle_d18.421689
X-RAY DIFFRACTIONf_chiral_restr0.084317
X-RAY DIFFRACTIONf_plane_restr0.004310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54050.2751290.23132517X-RAY DIFFRACTION95
1.5405-1.58590.22281340.21052553X-RAY DIFFRACTION96
1.5859-1.6370.24811280.20612576X-RAY DIFFRACTION97
1.637-1.69550.21361480.18472541X-RAY DIFFRACTION97
1.6955-1.76330.22071370.18952612X-RAY DIFFRACTION97
1.7633-1.84350.23631500.18172580X-RAY DIFFRACTION97
1.8435-1.94060.19671350.17312622X-RAY DIFFRACTION98
1.9406-2.06210.17511190.16282627X-RAY DIFFRACTION98
2.0621-2.22110.18531540.16122607X-RAY DIFFRACTION98
2.2211-2.44420.19631480.17512617X-RAY DIFFRACTION98
2.4442-2.79690.1881420.1792631X-RAY DIFFRACTION98
2.7969-3.52020.17391490.16972657X-RAY DIFFRACTION98
3.5202-19.13120.15131280.16922678X-RAY DIFFRACTION97

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