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- PDB-6iei: Loop deletion and proline insertion mutant (deleting six residues... -

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Basic information

Entry
Database: PDB / ID: 6iei
TitleLoop deletion and proline insertion mutant (deleting six residues and inserted five proline residues)
ComponentsOuter surface protein A
KeywordsDE NOVO PROTEIN / Outer surface protein A / OspA / LIPID BINDING PROTEIN
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 B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShiga, S. / Makabe, K.
CitationJournal: Chembiochem / Year: 2019
Title: Domain-Swapping Design by Polyproline Rod Insertion.
Authors: Shiga, S. / Yamanaka, M. / Fujiwara, W. / Hirota, S. / Goda, S. / Makabe, K.
History
DepositionSep 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 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)26,3491
Polymers26,3491
Non-polymers00
Water54030
1
A: Outer surface protein A

A: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)52,6972
Polymers52,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3710 Å2
ΔGint-31 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.381, 79.381, 105.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Outer surface protein A


Mass: 26348.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi B31 (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.: 30 / 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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.6 M Ammonium sulfate, 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 28975 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 28.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1401 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.603 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.241
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The authors scaled the sample data as P3, but refined the data as P321.
RfactorNum. reflection% reflectionSelection details
Rfree0.27558 794 5.1 %RANDOM
Rwork0.22009 ---
obs0.22291 14666 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.977 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å21.02 Å20 Å2
2--2.04 Å2-0 Å2
3----6.63 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 0 30 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021860
X-RAY DIFFRACTIONr_bond_other_d0.0060.021836
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9932509
X-RAY DIFFRACTIONr_angle_other_deg0.94334285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.81427.79759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36715366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.06152
X-RAY DIFFRACTIONr_chiral_restr0.0770.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022054
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
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_it4.8396.072999
X-RAY DIFFRACTIONr_mcbond_other4.8336.069998
X-RAY DIFFRACTIONr_mcangle_it6.7649.0881247
X-RAY DIFFRACTIONr_mcangle_other6.7669.0911248
X-RAY DIFFRACTIONr_scbond_it6.3096.766861
X-RAY DIFFRACTIONr_scbond_other6.3086.766861
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4439.8081262
X-RAY DIFFRACTIONr_long_range_B_refined11.39357.5247356
X-RAY DIFFRACTIONr_long_range_B_other11.39757.537352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.404→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 80 -
Rwork0.337 1009 -
obs--99.82 %

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