+Open data
-Basic information
Entry | Database: PDB / ID: 1lgn | |||||||||
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Title | DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT | |||||||||
Components | SERUM AMYLOID P COMPONENT | |||||||||
Keywords | SERUM PROTEIN / AMYLOIDOSIS / DRUG DESIGN / NUCLEOTIDE | |||||||||
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: 2.8 Å | |||||||||
Authors | Hohenester, E. / Pepys, M.B. / Wood, S.P. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP. Authors: Hohenester, E. / Hutchinson, W.L. / Pepys, M.B. / Wood, S.P. #1: Journal: Nature / Year: 1994 Title: Structure of Pentameric Human Serum Amyloid P Component Authors: Emsley, J. / White, H.E. / O'Hara, B.P. / Oliva, G. / Srinivasan, N. / Tickle, I.J. / Blundell, T.L. / 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 | 1lgn.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lgn.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lgn_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 1lgn_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 1lgn_validation.xml.gz | 37 KB | Display | |
Data in CIF | 1lgn_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/1lgn ftp://data.pdbj.org/pub/pdb/validation_reports/lg/1lgn | HTTPS FTP |
-Related structure data
Related structure data | 1sacS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Details | SAP IS A PENTAMER OF IDENTICAL SUBUNITS. |
-Components
#1: Protein | Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P02743 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-D5M / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 71 % Description: THE DIFFRACTION LIMIT IS VERY ANISOTROPIC (BETTER THAN 2.8 A ALONG A* AND B*, APPROXIMATELY 3.5 A ALONG C*) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3 + 3 UL HANGING DROPS AT 277K PROTEIN SOLUTION: 20 MG/ML PROTEIN, 10 MM TRIS-HCL, PH 8.0, 140 MM NACL, 20 MM DAMP, 0.02 % NA-AZIDE. RESERVOIR SOLUTION: 100 MM BIS-TRIS PROPANE- HCL PH 8.0, ...Details: 3 + 3 UL HANGING DROPS AT 277K PROTEIN SOLUTION: 20 MG/ML PROTEIN, 10 MM TRIS-HCL, PH 8.0, 140 MM NACL, 20 MM DAMP, 0.02 % NA-AZIDE. RESERVOIR SOLUTION: 100 MM BIS-TRIS PROPANE- HCL PH 8.0, 20 MM CALCIUM CHLORIDE, 12-14 % (W/V) POLYETHYLENEGLYCOL 4000., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 366263 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.4 / % possible all: 97.5 |
Reflection | *PLUS Num. obs: 53133 / Num. measured all: 366263 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SAC WITHOUT WATER MOLECULES AND ACETATE IONS, ALL B-FACTORS SET TO 40 A**2 Resolution: 2.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: SEE REMARKS / Cross valid method: FREE R / σ(F): 0 Details: 15 THIN RESOLUTION SHELLS WERE DEFINED FOR THE CALCULATION OF THE FREE R VALUE USING XDLDATAMAN (CCP4).
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Displacement parameters | Biso mean: 50 Å2
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Refine analyze | Luzzati sigma a obs: 0.51 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.454 |