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Yorodumi- PDB-1nzi: Crystal Structure of the CUB1-EGF Interaction Domain of Complemen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nzi | ||||||
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Title | Crystal Structure of the CUB1-EGF Interaction Domain of Complement Protease C1s | ||||||
Components | Complement C1s component | ||||||
Keywords | HYDROLASE / CALCIUM / COMPLEMENT / INNATE IMMUNITY / MODULAR STRUCTURE / CUB / EGF | ||||||
Function / homology | Function and homology information complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis ...complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Gregory, L.A. / Thielens, N.M. / Arlaud, G.J. / Fontecilla-Camps, J.C. / Gaboriaud, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: X-ray structure of the Ca2+-binding interaction domain of C1s. Insights into the assembly of the C1 complex of complement Authors: Gregory, L.A. / Thielens, N.M. / Arlaud, G.J. / Fontecilla-Camps, J.C. / Gaboriaud, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nzi.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nzi.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 1nzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nzi_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 1nzi_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 1nzi_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1nzi_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzi ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzi | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 calcium-dependent homodimer in the asymmetric unit |
-Components
#1: Protein | Mass: 18144.895 Da / Num. of mol.: 2 / Fragment: CALCIUM-DEPENDENT INTERACTION DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Cell line (production host): HIGH FIVE INSECT CELLS / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P09871, complement subcomponent C_overbar_1s_ #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, magnesium chloride, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 52134 / Num. obs: 52134 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Rsym value: 0.143 / % possible all: 93.3 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 52518 / Redundancy: 3.5 % / Num. measured all: 181271 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 93.3 % / Redundancy: 2.2 % / Num. unique obs: 7588 / Num. measured obs: 16763 / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD, molecular replacement / Resolution: 1.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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LS refinement shell | Resolution: 1.5→1.58 Å / Rfactor Rfree error: 0.01
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Refinement | *PLUS Highest resolution: 1.5 Å / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.229 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |