+Open data
-Basic information
Entry | Database: PDB / ID: 1qqf | ||||||
---|---|---|---|---|---|---|---|
Title | N-TERMINALLY TRUNCATED C3D,G FRAGMENT OF THE COMPLEMENT SYSTEM | ||||||
Components | PROTEIN (COMPLEMENT C3DG) | ||||||
Keywords | IMMUNE SYSTEM / ALPHA-ALPHA BARREL / COMPLEMENT | ||||||
Function / homology | Function and homology information Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / tolerance induction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / vascular associated smooth muscle cell differentiation / Peptide ligand-binding receptors / oviduct epithelium development ...Alternative complement activation / Activation of C3 and C5 / Regulation of Complement cascade / tolerance induction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / vascular associated smooth muscle cell differentiation / Peptide ligand-binding receptors / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of developmental growth / positive regulation of phagocytosis, engulfment / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / G alpha (i) signalling events / complement activation, alternative pathway / complement activation / Neutrophil degranulation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / response to magnesium ion / positive regulation of vascular endothelial growth factor production / positive regulation of phagocytosis / complement activation, classical pathway / response to glucocorticoid / fatty acid metabolic process / response to progesterone / response to bacterium / positive regulation of receptor-mediated endocytosis / response to estrogen / positive regulation of angiogenesis / chemotaxis / response to estradiol / retina development in camera-type eye / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / inflammatory response / positive regulation of protein phosphorylation / lipid binding / cell surface / protein-containing complex / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å | ||||||
Authors | Zanotti, G. / Bassetto, A. / Battistutta, R. / Stoppini, M. / Berni, R. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2000 Title: Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment. Authors: Zanotti, G. / Bassetto, A. / Battistutta, R. / Folli, C. / Arcidiaco, P. / Stoppini, M. / Berni, R. #1: Journal: Science / Year: 1998 Title: X-Ray Crystal Structure of C3D: A C3 Fragment and Ligand for Complement Receptor 2 Authors: Nagar, B. / Jones, R.G. / Diefenbach, R.J. / Isenman, D.E. / Rini, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qqf.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qqf.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqf ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqf | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | dimer generated from the monomer of the asymmetric unit and a second monomer related to the first by a crystallographic twofold axis |
-Components
#1: Protein | Mass: 31167.398 Da / Num. of mol.: 1 / Fragment: N-TERMINALLY TRUNCATED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: PLASMA / References: UniProt: P01026 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 / Details: 24% PEG 6000, K PHOSPHATE 50 MM, pH 7.0 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 38 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, sitting dropDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→26.9 Å / Num. obs: 50041 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 8.04 |
Reflection shell | Resolution: 1.45→1.62 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.285 / % possible all: 97.2 |
Reflection shell | *PLUS % possible obs: 97.2 % / Num. unique obs: 13685 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.45→10 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC B FACTORS IN THE LAST CYCLES
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.212 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|