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Yorodumi- PDB-2odp: Complement component C2a, the catalytic fragment of C3- and C5-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2odp | |||||||||
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Title | Complement component C2a, the catalytic fragment of C3- and C5-convertase of human complement | |||||||||
Components | Complement C2 | |||||||||
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 complex / classical-complement-pathway C3/C5 convertase / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / response to nutrient / complement activation, classical pathway / Regulation of Complement cascade ...classical-complement-pathway C3/C5 convertase complex / classical-complement-pathway C3/C5 convertase / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / response to nutrient / complement activation, classical pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 2odp.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2odp.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 2odp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2odp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2odp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2odp_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 2odp_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/2odp ftp://data.pdbj.org/pub/pdb/validation_reports/od/2odp | HTTPS FTP |
-Related structure data
Related structure data | 2odqSC 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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Details | The biological assembly is a monomer |
-Components
-Protein , 1 types, 1 molecules A
#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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-Sugars , 3 types, 4 molecules
#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 |
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#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 |
-Non-polymers , 2 types, 260 molecules
#5: Chemical | ChemComp-MG / |
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#6: 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: 2.82 Å3/Da / Density % sol: 56.35 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97969 Å |
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Jun 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97969 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50.48 Å / Num. obs: 49897 / % possible obs: 98 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 7.1 / Rsym value: 0.17 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ODQ Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.166 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.319 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.905→1.955 Å / Total num. of bins used: 20
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