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- PDB-2oyb: The crystal structure of OspA mutant -

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Basic information

Entry
Database: PDB / ID: 2oyb
TitleThe crystal structure of OspA mutant
ComponentsOuter surface protein A
KeywordsMEMBRANE PROTEIN / beta-sheet
Function / homology
Function and homology information


cell outer membrane / cell surface / membrane / metal ion binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMakabe, K. / Biancalana, M. / Terechko, V. / Koide, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics
Authors: Biancalana, M. / Makabe, K. / Koide, A. / Koide, S.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,5721
Polymers26,5721
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.125, 54.686, 66.466
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer surface protein A


Mass: 26571.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: ospA / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45040, UniProt: P0CL66*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 37% PEG400, 0.1M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 57675 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.01
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.36 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G8C

2g8c


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.447 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 2900 5.1 %RANDOM
Rwork0.15535 ---
all0.15709 54499 --
obs0.15709 54499 99.83 %-
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: 11.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.07 Å2
2---0.11 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 0 445 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221855
X-RAY DIFFRACTIONr_bond_other_d0.0010.021691
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9842510
X-RAY DIFFRACTIONr_angle_other_deg0.74233996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45827.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.75715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.032152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_nbd_refined0.2070.2288
X-RAY DIFFRACTIONr_nbd_other0.1820.21541
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2927
X-RAY DIFFRACTIONr_nbtor_other0.0820.21050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.130.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6451.51576
X-RAY DIFFRACTIONr_mcbond_other0.5841.5517
X-RAY DIFFRACTIONr_mcangle_it2.02121985
X-RAY DIFFRACTIONr_scbond_it3.0543725
X-RAY DIFFRACTIONr_scangle_it4.1564.5521
X-RAY DIFFRACTIONr_rigid_bond_restr1.36334105
X-RAY DIFFRACTIONr_sphericity_free5.2553446
X-RAY DIFFRACTIONr_sphericity_bonded3.16633530
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 231 -
Rwork0.159 3988 -
obs--99.69 %

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