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- PDB-6j6c: Borrelia burgdorferi OspA via surface entropy reduction (form3) -

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Basic information

Entry
Database: PDB / ID: 6j6c
TitleBorrelia burgdorferi OspA via surface entropy reduction (form3)
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: 1.6 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
Water4,360242
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 area13430 Å2
Unit cell
Length a, b, c (Å)33.197, 54.316, 65.773
Angle α, β, γ (deg.)90.00, 100.49, 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: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,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 / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Imidazole pH 7.0, 45% 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: 1.6→20 Å / Num. obs: 30494 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 1490 / % possible all: 100

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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: 1.6→19.715 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 1707 5.62 %RANDOM
Rwork0.1866 ---
obs0.1879 30360 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 242 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061847
X-RAY DIFFRACTIONf_angle_d0.872499
X-RAY DIFFRACTIONf_dihedral_angle_d17.817695
X-RAY DIFFRACTIONf_chiral_restr0.057319
X-RAY DIFFRACTIONf_plane_restr0.004312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.241370.22142372X-RAY DIFFRACTION99
1.6471-1.70020.24561400.2122337X-RAY DIFFRACTION100
1.7002-1.7610.25631330.19862406X-RAY DIFFRACTION100
1.761-1.83140.24831210.19992408X-RAY DIFFRACTION100
1.8314-1.91470.21021360.1852367X-RAY DIFFRACTION100
1.9147-2.01560.18741290.17742397X-RAY DIFFRACTION100
2.0156-2.14170.19871280.17882405X-RAY DIFFRACTION100
2.1417-2.30680.1981650.17532363X-RAY DIFFRACTION100
2.3068-2.53850.20611440.18972407X-RAY DIFFRACTION100
2.5385-2.90490.21651470.18542375X-RAY DIFFRACTION100
2.9049-3.6560.19431770.18432387X-RAY DIFFRACTION100
3.656-19.71650.21361500.18752429X-RAY DIFFRACTION99

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