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- PDB-5b2a: Crystal structure of a mutant of OspA -

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Basic information

Entry
Database: PDB / ID: 5b2a
TitleCrystal structure of a mutant of OspA
ComponentsOuter surface protein A
KeywordsMEMBRANE PROTEIN / beta-sheet / amyloid
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 speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsHori , Y. / 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 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
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
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13570 Å2
Unit cell
Length a, b, c (Å)33.370, 53.658, 65.756
Angle α, β, γ (deg.)90.00, 100.35, 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 / Fragment: UNP RESIDUES 27-273
Mutation: E37S,E45S,K48A,K64S,K83A,E104S,K107S,S120V,S121L,T122G,E123D,E196A,K239S,E240S,K254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: ospA / Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 40% PEG 400, 0.1M Tris pH 9.0

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Data collection

DiffractionMean temperature: 100 K
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: 1.6→20 Å / Num. obs: 27889 / % possible obs: 97.18 % / Redundancy: 3.6 % / Net I/σ(I): 27.7
Reflection shellResolution: 1.6→1.63 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Cootmodel building
RefinementResolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.515 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25013 1483 5 %RANDOM
Rwork0.2008 ---
obs0.20333 27889 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.359 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0 Å20.42 Å2
2--3.48 Å2-0 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 192 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021827
X-RAY DIFFRACTIONr_bond_other_d0.0010.021820
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9892467
X-RAY DIFFRACTIONr_angle_other_deg0.88234235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27927.93158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95515362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.067152
X-RAY DIFFRACTIONr_chiral_restr0.1190.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9783.153987
X-RAY DIFFRACTIONr_mcbond_other2.9663.151986
X-RAY DIFFRACTIONr_mcangle_it3.8224.7271233
X-RAY DIFFRACTIONr_mcangle_other3.8294.7281234
X-RAY DIFFRACTIONr_scbond_it4.3753.582840
X-RAY DIFFRACTIONr_scbond_other4.3733.581840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4355.161232
X-RAY DIFFRACTIONr_long_range_B_refined7.34425.9382028
X-RAY DIFFRACTIONr_long_range_B_other7.32625.5591977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 127 -
Rwork0.337 1879 -
obs--91.06 %

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