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- PDB-5z1o: Crystal structure of an OspA mutant -

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Basic information

Entry
Database: PDB / ID: 5z1o
TitleCrystal structure of an OspA mutant
ComponentsOuter Surface Protein A
KeywordsMEMBRANE PROTEIN / Outer surface protein A / OspA / DE NOVO PROTEIN
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 Å
AuthorsTakada, S. / Makabe, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
kakenhi Japan
CitationJournal: To Be Published
Title: Crystal structure of an OspA mutant.
Authors: Takada, S. / Makabe, K.
History
DepositionDec 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 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 / 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
B: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)68,9292
Polymers68,9292
Non-polymers00
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-6 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.140, 81.731, 110.344
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer Surface Protein A


Mass: 34464.344 Da / Num. of mol.: 2 / Mutation: L112A, L135F, E158A, K160Y, L181A
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.: 520 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 28% PEG 400, 0.1M Tris-HCl pH 8.8

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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: May 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43536 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 3.48
Reflection shellResolution: 2→2.03 Å

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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→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.887 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26221 2184 5 %RANDOM
Rwork0.20298 ---
obs0.20593 41289 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.661 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å2-0 Å20.04 Å2
2---0.85 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 0 520 5300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024822
X-RAY DIFFRACTIONr_bond_other_d0.0060.024666
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9846488
X-RAY DIFFRACTIONr_angle_other_deg0.925310860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79126.591176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43315948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6961510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025356
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02918
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_it2.253.1732526
X-RAY DIFFRACTIONr_mcbond_other2.253.1732525
X-RAY DIFFRACTIONr_mcangle_it3.564.7423154
X-RAY DIFFRACTIONr_mcangle_other3.564.7423155
X-RAY DIFFRACTIONr_scbond_it2.3023.4912296
X-RAY DIFFRACTIONr_scbond_other2.3023.4922296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7515.0753334
X-RAY DIFFRACTIONr_long_range_B_refined6.82826.0135485
X-RAY DIFFRACTIONr_long_range_B_other6.43425.4845291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.996→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 149 -
Rwork0.225 2883 -
obs--95.77 %

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