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- PDB-4wre: 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: 4wre | ||||||
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Title | Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D) Complexed with Inositol | ||||||
![]() | 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 | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 444.1 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wr9C ![]() 4wrcSC ![]() 4wrfC ![]() 4wuwC ![]() 4wuxC 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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Details | biological unit is the same as asym. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16633.369 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: E171D/P175E/N187S/R197N/K203D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 92 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/INS.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/INS.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-INS / | #4: Chemical | ChemComp-HEZ / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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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 with 2% (w/v) inositol for 30 minutes |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→15 Å / Num. obs: 14452 / % possible obs: 98.4 % / Redundancy: 5 % / Biso Wilson estimate: 28.98 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.639 / Net I/av σ(I): 21.833 / Net I/σ(I): 27.4 / Num. measured all: 72216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code 4WRC Resolution: 1.751→14.592 Å / FOM work R set: 0.8612 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.61 / 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: 70.6 Å2 / Biso mean: 23.02 Å2 / Biso min: 9.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.751→14.592 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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