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- PDB-5ys7: Crystal structure of an OspA mutant -

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Basic information

Entry
Database: PDB / ID: 5ys7
TitleCrystal structure of an OspA mutant
ComponentsOuter Surface Protein A
KeywordsDE NOVO PROTEIN / outer surface protein A / OspA
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Outer Surface Protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTakada, S. / Makabe, K.
CitationJournal: To Be Published
Title: Crystal structure of an OspA mutant
Authors: Takada, S. / Makabe, K.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: 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 / 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

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Assembly

Deposited unit
A: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)34,5401
Polymers34,5401
Non-polymers00
Water4,900272
1
A: Outer Surface Protein A

A: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)69,0812
Polymers69,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2470 Å2
ΔGint-12 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.279, 107.988, 36.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Outer Surface Protein A


Mass: 34540.438 Da / Num. of mol.: 1 / Mutation: L112A, L135A, E158F, K160Y, L181F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M Tris-HCl, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / 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: 2.1→20 Å / Num. obs: 20560 / % possible obs: 99.8 % / Redundancy: 10.3 % / Net I/σ(I): 29.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1032 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKA

3cka


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.346 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25999 1039 5.1 %RANDOM
Rwork0.19615 ---
obs0.1994 19458 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-0 Å2
2--0.99 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 0 272 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022409
X-RAY DIFFRACTIONr_bond_other_d0.0020.022324
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9833242
X-RAY DIFFRACTIONr_angle_other_deg0.94635408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32926.51789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62115471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.02155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
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_it2.2253.3591259
X-RAY DIFFRACTIONr_mcbond_other2.2233.3591258
X-RAY DIFFRACTIONr_mcangle_it3.3295.0251572
X-RAY DIFFRACTIONr_mcangle_other3.3295.0251573
X-RAY DIFFRACTIONr_scbond_it2.8243.7641149
X-RAY DIFFRACTIONr_scbond_other2.8233.7651149
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5495.4651669
X-RAY DIFFRACTIONr_long_range_B_refined6.61727.6022723
X-RAY DIFFRACTIONr_long_range_B_other6.52727.2192628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.087→2.141 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 72 -
Rwork0.226 1280 -
obs--90.8 %

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