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Yorodumi- PDB-5hyu: Structure of human C4b-binding protein alpha chain CCP domains 1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hyu | |||||||||||||||
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Title | Structure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M2 protein | |||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / M protein / Complement / Streptococcus pyogenes / hypervariable antigen | |||||||||||||||
Function / homology | Function and homology information regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / phagocytosis / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response ...regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / phagocytosis / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / extracellular space / RNA binding / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Streptococcus pyogenes (bacteria) Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.561 Å | |||||||||||||||
Authors | Buffalo, C.Z. / Bahn-Suh, A.J. / Ghosh, P. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Microbiol / Year: 2016 Title: Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Authors: Buffalo, C.Z. / Bahn-Suh, A.J. / Hirakis, S.P. / Biswas, T. / Amaro, R.E. / Nizet, V. / Ghosh, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hyu.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hyu.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyu ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12759.146 Da / Num. of mol.: 1 / Fragment: UNP residues 42-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: emmL2.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P50468 |
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#2: Protein | Mass: 14163.894 Da / Num. of mol.: 1 / Fragment: UNP residues 49-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C4BPA, C4BP / Production host: Escherichia coli (E. coli) / References: UniProt: P04003 |
#3: 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: 5.05 Å3/Da / Density % sol: 75.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.5 M Ammonium Sulfate, 0.1 M Bis-Tris Propane |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.56→50 Å / Num. obs: 18572 / % possible obs: 100 % / Redundancy: 42.8 % / CC1/2: 1 / Rmerge(I) obs: 0.18 / Net I/σ(I): 67.6 | |||||||||||||||
Reflection shell | Resolution: 2.56→2.6 Å / Redundancy: 43.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 4.17 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.561→35.971 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.561→35.971 Å
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Refine LS restraints |
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LS refinement shell |
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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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