+Open data
-Basic information
Entry | Database: PDB / ID: 1pk6 | ||||||
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Title | Globular Head of the Complement System Protein C1q | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complement system / C1q / immunology / jellyroll / IgG | ||||||
Function / homology | Function and homology information complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation ...complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation / neuron remodeling / Initial triggering of complement / astrocyte activation / complement activation, classical pathway / Regulation of Complement cascade / synapse organization / microglial cell activation / cell-cell signaling / amyloid-beta binding / collagen-containing extracellular matrix / postsynapse / blood microparticle / immune response / innate immune response / synapse / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Gaboriaud, C. / Juanhuix, J. / Gruez, A. / Lacroix, M. / Darnault, C. / Pignol, D. / Verger, D. / Fontecilla-Camps, J.C. / Arlaud, G.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The crystal structure of the globular head of complement protein C1q provides a basis for its versatile recognition properties. Authors: Gaboriaud, C. / Juanhuix, J. / Gruez, A. / Lacroix, M. / Darnault, C. / Pignol, D. / Verger, D. / Fontecilla-Camps, J.C. / Arlaud, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pk6.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pk6.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pk6_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 1pk6_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 1pk6_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1pk6_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/1pk6 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/1pk6 | HTTPS FTP |
-Related structure data
Related structure data | 1gr3S 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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-Components
#1: Protein | Mass: 14914.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02745 |
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#2: Protein | Mass: 14996.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02746 |
#3: Protein | Mass: 14302.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02747 |
#4: Chemical | ChemComp-CA / |
#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: 2.03 Å3/Da / Density % sol: 39.34 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, CaCl2, B-mercaptoethanol, agarose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.6 / 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: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC / Detector: CCD / Date: Jan 28, 1998 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25.4 Å / Num. all: 26237 / Num. obs: 26090 / % possible obs: 90 % / Redundancy: 4.73 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.86→1.98 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.7 / % possible all: 67.2 |
Reflection | *PLUS Lowest resolution: 26 Å / Num. measured all: 116591 |
Reflection shell | *PLUS Highest resolution: 1.85 Å / % possible obs: 67.2 % / Num. unique obs: 3614 / Num. measured obs: 3946 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 1GR3 Resolution: 1.85→25.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.396 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A90, A92, A160, B92, B93, B108, B109, B150, B163, B165, C89 HAVE DIFFUSE LATERAL CHAINS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.877 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→25.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.898 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 26 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.98 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.28 |