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Yorodumi- PDB-6hpn: Crystal structure of Borrelia spielmanii WP_012665240 (BSA64) - a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hpn | ||||||
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Title | Crystal structure of Borrelia spielmanii WP_012665240 (BSA64) - an orthologous protein to B. burgdorferi BBA64 | ||||||
Components | Antigen, P35 | ||||||
Keywords | MEMBRANE PROTEIN / Outer surface protein / PFam54. | ||||||
Function / homology | Bbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha / Antigen, P35 Function and homology information | ||||||
Biological species | Borreliella spielmanii A14S (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Brangulis, K. / Akopjana, I. / Kazaks, A. / Tars, K. | ||||||
Funding support | Latvia, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Structural analysis of the outer surface proteins from Borrelia burgdorferi paralogous gene family 54 that are thought to be the key players in the pathogenesis of Lyme disease. 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 | 6hpn.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hpn.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 6hpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hpn_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 6hpn_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 6hpn_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6hpn_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hpn ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hpn | HTTPS FTP |
-Related structure data
Related structure data | 4alyS S: Starting model for refinement |
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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: 25876.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First 4 residues (GAMG) are the remnants from the expression tag. Source: (gene. exp.) Borreliella spielmanii A14S (bacteria) / Gene: BSPA14S_A0059 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0RC68 |
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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: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1 M Sodium citrate 15% 2-propanol 18% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43.25 Å / Num. obs: 10298 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9 / Num. unique obs: 1470 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ALY Resolution: 2.6→43.25 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.987 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.429 / ESU R Free: 0.271 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: 68.08 Å2 / Biso mean: 24.556 Å2 / Biso min: 12 Å2
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Refinement step | Cycle: final / Resolution: 2.6→43.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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