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Yorodumi- PDB-6zh1: Crystal structure of complex between FH19-20 and FhbA protein fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zh1 | |||||||||
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Title | Crystal structure of complex between FH19-20 and FhbA protein from Borrelia hermsii | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Innate immunity / complement / relapsing fever / Lyme disease | |||||||||
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 hermsii YOR (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | |||||||||
Authors | Kogan, K. / Kotila, T. / Meri, T. / Goldman, A. | |||||||||
Funding support | Finland, United Kingdom, 2items
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Citation | Journal: Plos Pathog. / Year: 2022 Title: Mechanism of Borrelia immune evasion by FhbA-related proteins. Authors: Kogan, K. / Haapasalo, K. / Kotila, T. / Moore, R. / Lappalainen, P. / Goldman, A. / Meri, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zh1.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zh1.ent.gz | 107.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zh1_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 6zh1_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 6zh1_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 6zh1_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/6zh1 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/6zh1 | HTTPS FTP |
-Related structure data
Related structure data | 2g7iS 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: 22148.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Factor H-binding protein A / Source: (gene. exp.) Borrelia hermsii YOR (bacteria) / Gene: BHY_1174 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W5SB08 | ||||||
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#2: Protein | Mass: 15084.103 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P08603 | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.1 M MES pH6.7, 0.2 M Ammonium Sulfate, 20% (v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.828 Å / Num. obs: 20180 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 49.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.047 / Rrim(I) all: 0.172 / Net I/av σ(I): 12.531 / Net I/σ(I): 12.531 |
Reflection shell | Resolution: 2.2→2.237 Å / Redundancy: 13.78 % / Rmerge(I) obs: 2.436 / Mean I/σ(I) obs: 1 / Num. unique obs: 993 / CC1/2: 0.513 / Rpim(I) all: 0.673 / Rrim(I) all: 2.529 / % possible all: 99 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G7I Resolution: 2.2→22.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.187
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Displacement parameters | Biso max: 160.42 Å2 / Biso mean: 59.9 Å2 / Biso min: 27.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→22.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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