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Yorodumi- PDB-6j5r: OspA mutant, PSAM-VLGDV1-form8, grafted short chameleon sequence ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j5r | ||||||
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Title | OspA mutant, PSAM-VLGDV1-form8, grafted short chameleon sequence from alpha-B crystallin | ||||||
Components | Outer surface protein A | ||||||
Keywords | LIPID BINDING PROTEIN / Peptide Self-Assembly Mimic / single-layer beta-sheet / chameleon sequence | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borreliella burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Fujiwara, H. / Makabe, K. | ||||||
Citation | Journal: J Mol Liq / Year: 2019 Title: Beta-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals Authors: Fujiwara, H. / Hongo, K. / Hori, Y. / Yoshida, N. / Makabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j5r.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j5r.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/6j5r ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j5r | HTTPS FTP |
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-Related structure data
Related structure data | 5b2aC 6j5mC 6j5nC 6j5oC 6j5pC 6j5qC 6j6bC 6j6cC 6j6dC 6j6eC 6j47S 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: 26345.543 Da / Num. of mol.: 1 Mutation: E37S, E45S, K46S,K64S, E104S, K107S, K239S, E240S, K254S, K48A, K60A, K83A, E196A, S120V,S121L, T122G, E123D, E124V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Gene: ospA / Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS |
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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: 2.13 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tri-HCl pH 8.5, 38% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 18781 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 863 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J47 Resolution: 1.85→19.685 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 29.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.685 Å
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Refine LS restraints |
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LS refinement shell |
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