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Yorodumi- PDB-6rjx: Crystal structure of the N-terminal domain of Lyme disease agent ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rjx | ||||||
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Title | Crystal structure of the N-terminal domain of Lyme disease agent Borrelia burgdorferi major virulence factor BB0323 (native data) | ||||||
Components | LysM domain protein | ||||||
Keywords | STRUCTURAL PROTEIN / lipoprotein / spectrin repeats | ||||||
Function / homology | LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / LysM domain protein Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Brangulis, K. / Akopjana, I. / Kazaks, A. / Tars, K. | ||||||
Funding support | Latvia, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Crystal structure of the N-terminal domain of the major virulence factor BB0323 from the Lyme disease agent Borrelia burgdorferi. Authors: Brangulis, K. / Akopjana, 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 | 6rjx.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rjx.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rjx_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 6rjx_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 6rjx_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6rjx_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/6rjx ftp://data.pdbj.org/pub/pdb/validation_reports/rj/6rjx | HTTPS FTP |
-Related structure data
Related structure data | 6rjwSC 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: 22249.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: the 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_0323 / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51302 |
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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: 1.93 Å3/Da / Density % sol: 36.24 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KNO3 18% 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: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→44 Å / Num. obs: 7543 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 729 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RJW Resolution: 2.35→44 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.197 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.268 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: 105.81 Å2 / Biso mean: 36.155 Å2 / Biso min: 20.81 Å2
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Refinement step | Cycle: final / Resolution: 2.35→44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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