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Yorodumi- PDB-5hyp: Structure of human C4b-binding protein alpha cain CCP domains 1 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hyp | |||||||||||||||
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Title | Structure of human C4b-binding protein alpha cain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M28 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 / cell wall / 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 / cell wall / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / RNA binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Streptococcus pyogenes (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.024 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 | 5hyp.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hyp.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hyp_validation.pdf.gz | 435.7 KB | Display | wwPDB validaton report |
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Full document | 5hyp_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 5hyp_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 5hyp_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyp ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyp | HTTPS FTP |
-Related structure data
Related structure data | 5hytC 5hyuSC 5hzpC 5i0qC S: Starting model for refinement C: citing same article (ref.) |
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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: 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 |
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#2: Protein | Mass: 12193.425 Da / Num. of mol.: 1 / Fragment: UNP residues 42-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: emm28 / Production host: Escherichia coli (E. coli) / References: UniProt: W0T1Y4 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.07 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→44.397 Å / Num. obs: 8361 / % possible obs: 99.8 % / Redundancy: 9.5 % / CC1/2: 0.48 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3.02→3.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.81 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HYU Resolution: 3.024→44.397 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.024→44.397 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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