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

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Basic information

Entry
Database: PDB / ID: 6idc
TitleLoop deletion and proline insertion mutant (deleting six residues and inserted six proline residues)
ComponentsOuter surface protein A
KeywordsDE NOVO PROTEIN / Outer surface protein A / 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 (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 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 9, 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)26,4461
Polymers26,4461
Non-polymers00
Water3,279182
1
A: Outer surface protein A

A: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)52,8912
Polymers52,8912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3740 Å2
ΔGint-30 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.383, 99.383, 102.289
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: 26445.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: ospA, BB_A15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0CL66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 5.51 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.5 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: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 75395 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3794 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 2.007→19.903 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.55 / Stereochemistry target values: ML
Details: The authors scaled the sample data as P3, but refined the data as P321.
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 2034 5.17 %RANDOM
Rwork0.2125 ---
obs0.2135 39369 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.007→19.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 182 2034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071868
X-RAY DIFFRACTIONf_angle_d0.822521
X-RAY DIFFRACTIONf_dihedral_angle_d2.9081163
X-RAY DIFFRACTIONf_chiral_restr0.055314
X-RAY DIFFRACTIONf_plane_restr0.005317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0069-2.05350.30181510.25242356X-RAY DIFFRACTION98
2.0535-2.10480.29661310.25542495X-RAY DIFFRACTION100
2.1048-2.16170.23971230.23752472X-RAY DIFFRACTION100
2.1617-2.22520.2761190.23912467X-RAY DIFFRACTION100
2.2252-2.29690.28071180.2412489X-RAY DIFFRACTION100
2.2969-2.37890.2951180.24612489X-RAY DIFFRACTION100
2.3789-2.4740.29031150.24332485X-RAY DIFFRACTION100
2.474-2.58640.27371320.25762475X-RAY DIFFRACTION100
2.5864-2.72240.32161210.25082479X-RAY DIFFRACTION100
2.7224-2.89250.24091380.25172503X-RAY DIFFRACTION100
2.8925-3.1150.29261320.2412506X-RAY DIFFRACTION100
3.115-3.42710.24851580.22912481X-RAY DIFFRACTION100
3.4271-3.91970.21841420.1892516X-RAY DIFFRACTION100
3.9197-4.9260.17851480.15932522X-RAY DIFFRACTION100
4.926-19.90420.19061880.19522600X-RAY DIFFRACTION100

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