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Yorodumi- PDB-4j38: Structure of Borrelia burgdorferi Outer surface protein E in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j38 | ||||||
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Title | Structure of Borrelia burgdorferi Outer surface protein E in complex with Factor H domains 19-20 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Beta barrel / Immune Evasion / Complement regulator binding / FH binding / Membrane / ERP PARALOG / LYME DISEASE / BBCRASP-3 | ||||||
Function / homology | Function and homology information regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Bhattacharjee, A. / Kolodziejczyk, R. / Kajander, T. / Goldman, A. / Jokiranta, T.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Basis for Complement Evasion by Lyme Disease Pathogen Borrelia burgdorferi Authors: Bhattacharjee, A. / Oeemig, J.S. / Kolodziejczyk, R. / Meri, T. / Kajander, T. / Lehtinen, M.J. / Iwai, H. / Jokiranta, T.S. / Goldman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j38.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j38.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j38 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j38 | HTTPS FTP |
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-Related structure data
Related structure data | 2m4fC 2g7iS C: citing same article (ref.) 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: 16941.975 Da / Num. of mol.: 1 / Fragment: UNP residues 21-171 Source method: isolated from a genetically manipulated source Details: Surface protein Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Strain: N40 / Gene: OspE / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: E4QGX1 |
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#2: Protein | Mass: 14614.674 Da / Num. of mol.: 1 / Fragment: FH domains 19-20, UNP residues 1103-1231 / Mutation: D1119G, Q1139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFH / Plasmid: pPICZalphaB / Production host: Komagataella pastoris (fungus) / References: UniProt: P08603 |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 3.68 Å3/Da / Density % sol: 66.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2M Ammonium sulfate, 0.1M Citric acid, 0.2M Sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97372 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011 |
Radiation | Monochromator: ESRF monochromator and torodial focusing mirro Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97372 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→50 Å / Num. obs: 12063 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.05 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.88 |
Reflection shell | Resolution: 2.83→2.9 Å / Redundancy: 7.08 % / Rmerge(I) obs: 1.098 / Mean I/σ(I) obs: 2.2 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2G7I Resolution: 2.83→19.509 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7954 / SU ML: 0.92 / σ(F): 2.01 / Phase error: 26.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.298 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.12 Å2 / Biso mean: 64.8 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→19.509 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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