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Yorodumi- PDB-6idc: Loop deletion and proline insertion mutant (deleting six residues... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6idc | ||||||
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Title | Loop deletion and proline insertion mutant (deleting six residues and inserted six proline residues) | ||||||
Components | Outer surface protein A | ||||||
Keywords | DE NOVO PROTEIN / Outer surface protein A / LIPID BINDING PROTEIN | ||||||
Function / homology | Outer 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 species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å | ||||||
Authors | Shiga, S. / Makabe, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6idc.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6idc.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 6idc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6idc_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
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Full document | 6idc_full_validation.pdf.gz | 423 KB | Display | |
Data in XML | 6idc_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6idc_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6idc ftp://data.pdbj.org/pub/pdb/validation_reports/id/6idc | HTTPS FTP |
-Related structure data
Related structure data | 6aisC 6icsC 6ieiC 6iysC 2g8cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.51 Å3/Da / Density % sol: 77.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.5 M Ammonium sulfate, 0.1 M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 75395 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.007→19.903 Å
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Refine LS restraints |
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LS refinement shell |
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