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Yorodumi- PDB-7mzt: Borrelia burgdorferi BBK32-C in complex with an autolytic fragmen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mzt | ||||||
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Title | Borrelia burgdorferi BBK32-C in complex with an autolytic fragment of human C1r at 4.1A | ||||||
Components |
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Keywords | PROTEIN BINDING / Lyme disease spirochete / Borrelia burgdorferi / complement system / classical pathway / protease inhibitor | ||||||
Function / homology | Function and homology information complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / fibronectin binding / serine-type peptidase activity / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle ...complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / fibronectin binding / serine-type peptidase activity / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / molecular adaptor activity / immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / 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: 4.07 Å | ||||||
Authors | Garcia, B.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Immunol. / Year: 2021 Title: A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes. Authors: Garrigues, R.J. / Powell-Pierce, A.D. / Hammel, M. / Skare, J.T. / Garcia, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mzt.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mzt.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/7mzt ftp://data.pdbj.org/pub/pdb/validation_reports/mz/7mzt | HTTPS FTP |
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-Related structure data
Related structure data | 2qy0S 6n1lS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19210.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00736 |
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#2: Protein | Mass: 27125.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00736 |
#3: Protein | Mass: 16922.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria) Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: bbk32, BB_K32 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50835 |
#4: Sugar | ChemComp-NAG / |
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: 2.39 Å3/Da / Density % sol: 48.7 % / Description: Small plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium formate, 27.5% Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.07→50 Å / Num. obs: 15139 / % possible obs: 85.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 92.77 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.164 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 4.07→4.25 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1455 / CC1/2: 0.903 / Rpim(I) all: 0.264 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qy0, 6n1l Resolution: 4.07→44.26 Å / SU ML: 0.7545 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.1386 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Author states that there is a second copy of complex in the asymmetric unit, evidenced by the electron density and the unit cell diemnsions. But it could not be modeled due to density ...Details: Author states that there is a second copy of complex in the asymmetric unit, evidenced by the electron density and the unit cell diemnsions. But it could not be modeled due to density disordering and dataset anisotropicity.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.07→44.26 Å
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Refine LS restraints |
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LS refinement shell |
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