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- PDB-4wrc: Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wrc | ||||||
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Title | Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D) | ||||||
![]() | Pulmonary surfactant-associated protein A | ||||||
![]() | SUGAR BINDING PROTEIN / COLLECTIN / CARBOHYDRATE BINDING / LECTIN / LIPID BINDING | ||||||
Function / homology | ![]() Signal regulatory protein family interactions / Surfactant metabolism / Toll Like Receptor 4 (TLR4) Cascade / Regulation of TLR by endogenous ligand / opsonization / response to interleukin-6 / respiratory gaseous exchange by respiratory system / collagen trimer / response to epidermal growth factor / response to vitamin A ...Signal regulatory protein family interactions / Surfactant metabolism / Toll Like Receptor 4 (TLR4) Cascade / Regulation of TLR by endogenous ligand / opsonization / response to interleukin-6 / respiratory gaseous exchange by respiratory system / collagen trimer / response to epidermal growth factor / response to vitamin A / cellular response to nitric oxide / response to hyperoxia / response to retinoic acid / response to glucocorticoid / positive regulation of phagocytosis / multivesicular body / response to hormone / circadian rhythm / cellular response to mechanical stimulus / carbohydrate binding / response to lipopolysaccharide / response to hypoxia / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rynkiewicz, M.J. / Wu, H. / Cafarella, T.R. / Nikolaidis, N.M. / Head, J.F. / Seaton, B.A. / McCormack, F.X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Differential ligand binding specificities of the pulmonary collectins are determined by the conformational freedom of a surface loop Authors: Rynkiewicz, M.J. / Wu, H. / Cafarella, T.R. / Nikolaidis, N.M. / Head, J.F. / Seaton, B.A. / McCormack, F.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.2 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wr9C ![]() 4wreC ![]() 4wrfC ![]() 4wuwC ![]() 4wuxC ![]() 3pakS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16633.369 Da / Num. of mol.: 1 / Mutation: E171D/P175E/N187S/R197N/K203D Source method: isolated from a genetically manipulated source Details: neck and carbohydrate recognition domain / Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEZ / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: DEDN (17 mg/ml) crystallized in hanging drops from a reservoir solution of 0.2 M calcium chloride and 14% (w/v) PEG 3,350. Before freezing, crystals were soaked in reservoir solution ...Details: DEDN (17 mg/ml) crystallized in hanging drops from a reservoir solution of 0.2 M calcium chloride and 14% (w/v) PEG 3,350. Before freezing, crystals were soaked in reservoir solution supplemented with 1.5 M 1,6-hexanediol as a cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 17, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→15 Å / Num. obs: 14534 / % possible obs: 99.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 32.26 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.65 / Net I/av σ(I): 39.492 / Net I/σ(I): 27.1 / Num. measured all: 155412 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code 3PAK Resolution: 1.8→13.644 Å / FOM work R set: 0.8326 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.71 Å2 / Biso mean: 32.45 Å2 / Biso min: 11.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→13.644 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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