[English] 日本語
Yorodumi- PDB-2w08: The structure of serum amyloid P component bound to 0-phospho- th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w08 | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of serum amyloid P component bound to 0-phospho- threonine | ||||||
Components | SERUM AMYLOID P-COMPONENT | ||||||
Keywords | GLYCOPROTEIN / POLYMORPHISM / METAL-BINDING / TAU / LECTIN / CALCIUM / AMYLOID / SECRETED / ALZHEIMERS | ||||||
Function / homology | Function and homology information negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell / virion binding ...negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell / virion binding / negative regulation of acute inflammatory response / chaperone-mediated protein complex assembly / acute-phase response / unfolded protein binding / protein folding / carbohydrate binding / collagen-containing extracellular matrix / blood microparticle / Amyloid fiber formation / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kolstoe, S.E. / Pepys, M.B. / Wood, S.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Molecular Dissection of Alzheimer'S Disease Neuropathology by Depletion of Serum Amyloid P Component. Authors: Kolstoe, S.E. / Ridha, B.H. / Bellotti, V. / Wang, N. / Robinson, C.V. / Crutch, S.J. / Keir, G. / Kukkastenvehmas, R. / Gallimore, J.R. / Hutchinson, W.L. / Hawkins, P.N. / Wood, S.P. / ...Authors: Kolstoe, S.E. / Ridha, B.H. / Bellotti, V. / Wang, N. / Robinson, C.V. / Crutch, S.J. / Keir, G. / Kukkastenvehmas, R. / Gallimore, J.R. / Hutchinson, W.L. / Hawkins, P.N. / Wood, S.P. / Rossor, M.N. / Pepys, M.B. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w08.cif.gz | 251.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w08.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w08_validation.pdf.gz | 485.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2w08_full_validation.pdf.gz | 502.2 KB | Display | |
Data in XML | 2w08_validation.xml.gz | 55.4 KB | Display | |
Data in CIF | 2w08_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w08 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w08 | HTTPS FTP |
-Related structure data
Related structure data | 1sacS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: O-PHOSPHOTHREONINE / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P02743 #2: Chemical | ChemComp-CA / #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-TPO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.39 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 0.06M TRIS-HCL PH8, 16% PEG 550MME, 0.01M CACL2, 0.08M NACL, 0.1% NAN3, 14.2MG/ML PROTEIN, 50MM LIGAND |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.67 Å / Num. obs: 140019 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.7→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 9.3 / % possible all: 95.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SAC Resolution: 1.7→47.48 Å / SU ML: 0.16 / σ(F): 0.04 / Phase error: 15.79 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.57 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→47.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|