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Yorodumi- PDB-6roc: Crystal structure of Borrelia burgdorferi outer surface protein B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6roc | ||||||
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Title | Crystal structure of Borrelia burgdorferi outer surface protein BBA69, mutant Leu214Met (Se-Met data) | ||||||
Components | Putative surface protein | ||||||
Keywords | MEMBRANE PROTEIN / Outer surface protein / PFam54 | ||||||
Function / homology | Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / membrane / Putative surface protein Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K. | ||||||
Funding support | Latvia, 1items
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Citation | Journal: Ticks Tick Borne Dis / Year: 2019 Title: Crystal structure of Borrelia burgdorferi outer surface protein BBA69 in comparison to the paralogous protein CspA. Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6roc.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6roc.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 6roc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6roc_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 6roc_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 6roc_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6roc_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/6roc ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6roc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22469.486 Da / Num. of mol.: 2 / Mutation: Leu214 mutated to Met Source method: isolated from a genetically manipulated source Details: First 4 residues (GAMG) are remnants from the expression tag. Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria) Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_A69 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50958 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M (NH4)2SO4 0.1M Tris pH 8.0 25% PEG 3350 |
-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: 0.9797 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2019 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.9→52.19 Å / Num. obs: 8521 / % possible obs: 96.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.2 | |||||||||||||||
Reflection shell | Resolution: 2.9→3.08 Å / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 1374 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→52.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 19.912 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.17 Å2 / Biso mean: 70.733 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.9→52.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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