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Yorodumi- PDB-2odq: Complement component C2a, the catalytic fragment of C3- and C5-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2odq | |||||||||
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Title | Complement component C2a, the catalytic fragment of C3- and C5-convertase of human complement | |||||||||
Components | Complement C2Complement component 2 | |||||||||
Keywords | HYDROLASE / Complement component C2a / C3/C5 convertase / complement serine protease / human complement system / glycoprotein / SP / vWFA | |||||||||
Function / homology | Function and homology information classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade ...classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade / response to bacterium / response to lipopolysaccharide / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Narayana, S.V.L. / Krishnan, V. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The crystal structure of c2a, the catalytic fragment of classical pathway c3 and c5 convertase of human complement. Authors: Krishnan, V. / Xu, Y. / Macon, K. / Volanakis, J.E. / Narayana, S.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2odq.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2odq.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 2odq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/2odq ftp://data.pdbj.org/pub/pdb/validation_reports/od/2odq | HTTPS FTP |
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-Related structure data
Related structure data | 2odpC 1rrkS 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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 57459.402 Da / Num. of mol.: 1 / Fragment: Complement C2a fragment / Mutation: C241A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five(BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P06681, UniProt: Q5JP69*PLUS, classical-complement-pathway C3/C5 convertase | ||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose | ||
#4: Sugar | #5: 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: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 10000, 0.1M HEPES, 0.3M glycyl-glycyl-glycine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 27904 / % possible obs: 98.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 7.1 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RRK Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.159 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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