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Yorodumi- PDB-4avs: Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component -
+Open data
-Basic information
Entry | Database: PDB / ID: 4avs | ||||||
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Title | Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component | ||||||
Components | SERUM AMYLOID P-COMPONENT | ||||||
Keywords | SUGAR BINDING PROTEIN / GLYCOPROTEIN / DISULFIDE BOND / LECTIN / METAL-BINDING | ||||||
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: 1.399 Å | ||||||
Authors | Kolstoe, S. / Wood, S.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc) Authors: Kolstoe, S.E. / Jenvey, M.C. / Purvis, A. / Light, M.E. / Thompson, D. / Hughes, P. / Pepys, M.B. / Wood, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4avs.cif.gz | 478 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4avs.ent.gz | 391.7 KB | Display | PDB format |
PDBx/mmJSON format | 4avs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4avs_validation.pdf.gz | 498.8 KB | Display | wwPDB validaton report |
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Full document | 4avs_full_validation.pdf.gz | 513.4 KB | Display | |
Data in XML | 4avs_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 4avs_validation.cif.gz | 78.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4avs ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avs | HTTPS FTP |
-Related structure data
Related structure data | 4avtC 4avvC 4ayuC 1sacS 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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-Components
#1: Protein | Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: SERUM / References: UniProt: P02743 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-N7P / #5: 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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.06 M TRIS-HCL, PH 8, 16% PEG 550 MME, 0.01 M CACL2, 0.08 M NACL AND 0.1% NAN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30.43 Å / Num. obs: 251592 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 8.47 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.5 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SAC Resolution: 1.399→30.479 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 13.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.227 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.399→30.479 Å
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Refine LS restraints |
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LS refinement shell |
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