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Yorodumi- PDB-8p32: BB0238 from Borrelia burgdorferi, Se-Met data for Leu240Met mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p32 | ||||||
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Title | BB0238 from Borrelia burgdorferi, Se-Met data for Leu240Met mutant | ||||||
Components | BB0238 | ||||||
Keywords | MEMBRANE PROTEIN / Lyme disease / borreliosis / outer surface protein / immune evasion | ||||||
Function / homology | membrane / Uncharacterized protein Function and homology information | ||||||
Biological species | Borreliella burgdorferi B31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Brangulis, K. / Foor, S.D. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Linden, S.B. / Altieri, A.S. / Akopjana, I. ...Brangulis, K. / Foor, S.D. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Linden, S.B. / Altieri, A.S. / Akopjana, I. / Baljinnyam, B. / Nelson, D.C. / Simeonov, A. / Herzberg, O. / Caimano, M.J. / Pal, U. | ||||||
Funding support | Latvia, 1items
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Citation | Journal: Mbio / Year: 2023 Title: A unique borrelial protein facilitates microbial immune evasion. Authors: Foor, S.D. / Brangulis, K. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Alreja, A.B. / Linden, S.B. / Altieri, A.S. / Baljinnyam, B. / Akopjana, I. / Nelson, D.C. / ...Authors: Foor, S.D. / Brangulis, K. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Alreja, A.B. / Linden, S.B. / Altieri, A.S. / Baljinnyam, B. / Akopjana, I. / Nelson, D.C. / Simeonov, A. / Herzberg, O. / Caimano, M.J. / Pal, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p32.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p32.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 8p32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p32_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
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Full document | 8p32_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 8p32_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 8p32_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/8p32 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p32 | HTTPS FTP |
-Related structure data
Related structure data | 8p33C 8sotC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16386.291 Da / Num. of mol.: 1 / Mutation: Leu240Met Source method: isolated from a genetically manipulated source Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage. There is a mutation Leu240Met introduced. Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0238 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51254 |
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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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.6 M ammonium sulfate 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→94.53 Å / Num. obs: 8541 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.15→2.21 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 9.8 / Num. unique obs: 674 / CC1/2: 0.982 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→47.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.262 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.63 Å2 / Biso mean: 38.948 Å2 / Biso min: 22.14 Å2
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Refinement step | Cycle: final / Resolution: 2.15→47.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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