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- PDB-6ais: Loop deletion mutant (deleting two residues) -

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Basic information

Entry
Database: PDB / ID: 6ais
TitleLoop deletion mutant (deleting two residues)
ComponentsOuter surface protein A
KeywordsDE NOVO PROTEIN / Outer surface protein A / OspA / LIPID BINDING PROTEIN
Function / homologyC1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer Surface Protein A; domain 3 / Lipocalin / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionAug 24, 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
O: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)26,2531
Polymers26,2531
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13530 Å2
Unit cell
Length a, b, c (Å)33.003, 54.876, 66.190
Angle α, β, γ (deg.)90.00, 100.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer surface protein A


Mass: 26253.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 45% w/v PEG400, 0.1 M Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 57159 / % possible obs: 99.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 15.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2864 / % possible all: 98.7

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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: 1.3→19.782 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 2801 4.92 %RANDOM
Rwork0.1763 ---
obs0.1776 56973 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→19.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 348 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051974
X-RAY DIFFRACTIONf_angle_d0.7932692
X-RAY DIFFRACTIONf_dihedral_angle_d3.1541134
X-RAY DIFFRACTIONf_chiral_restr0.085340
X-RAY DIFFRACTIONf_plane_restr0.004345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32240.26671460.23662692X-RAY DIFFRACTION99
1.3224-1.34650.2511340.2192630X-RAY DIFFRACTION99
1.3465-1.37230.221410.20822701X-RAY DIFFRACTION99
1.3723-1.40040.22581490.20382657X-RAY DIFFRACTION99
1.4004-1.43080.20941380.19522712X-RAY DIFFRACTION99
1.4308-1.46410.21321550.18962636X-RAY DIFFRACTION100
1.4641-1.50070.22731450.18972720X-RAY DIFFRACTION100
1.5007-1.54120.22261240.17842708X-RAY DIFFRACTION100
1.5412-1.58660.21711400.18282711X-RAY DIFFRACTION100
1.5866-1.63770.22331390.17752696X-RAY DIFFRACTION100
1.6377-1.69620.21311550.17372695X-RAY DIFFRACTION100
1.6962-1.76410.21171280.17272721X-RAY DIFFRACTION100
1.7641-1.84440.17651250.17112756X-RAY DIFFRACTION100
1.8444-1.94150.18991330.1672717X-RAY DIFFRACTION100
1.9415-2.0630.18951330.15722730X-RAY DIFFRACTION100
2.063-2.22210.15891390.15852704X-RAY DIFFRACTION100
2.2221-2.44540.18481230.17112734X-RAY DIFFRACTION100
2.4454-2.79840.20231430.17822742X-RAY DIFFRACTION100
2.7984-3.52240.21661560.17632724X-RAY DIFFRACTION100
3.5224-19.78380.19821550.17092786X-RAY DIFFRACTION100

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