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Yorodumi- PDB-4wuw: Crystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wuw | ||||||
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Title | Crystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E/K203D) Complexed with Inositol | ||||||
Components | Pulmonary surfactant-associated protein A | ||||||
Keywords | SUGAR BINDING PROTEIN / COLLECTIN / CARBOHYDRATE BINDING / LECTIN / LIPID BINDING | ||||||
Function / homology | Function and homology information Toll Like Receptor 4 (TLR4) Cascade / Signal regulatory protein family interactions / Surfactant metabolism / 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 ...Toll Like Receptor 4 (TLR4) Cascade / Signal regulatory protein family interactions / Surfactant metabolism / 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 / positive regulation of phagocytosis / response to glucocorticoid / 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.398 Å | ||||||
Authors | Rynkiewicz, M.J. / Wu, H. / Cafarella, T.R. / Nikolaidis, N.M. / Head, J.F. / Seaton, B.A. / McCormack, F.X. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wuw.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wuw.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 4wuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/4wuw ftp://data.pdbj.org/pub/pdb/validation_reports/wu/4wuw | HTTPS FTP |
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-Related structure data
Related structure data | 4wr9SC 4wrcC 4wreC 4wrfC 4wuxC C: citing same article (ref.) S: Starting model for refinement |
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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: 16708.461 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: E171D/P175E/N187S/K203D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sftpa1, Sftp-1, Sftp1, Sftpa / Plasmid: PVL 1392 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P08427 | ||
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#2: Chemical | ChemComp-INS / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.87 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: The crystals were grown in hanging drops using 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as the reservoir. Before freezing for x-ray ...Details: The crystals were grown in hanging drops using 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as the reservoir. Before freezing for x-ray data collection, crystals were soaked in reservoir solution of 10 mM calcium acetate without glycerol, but with stepwise additions of 5, 10, and 15% 2-methyl-2,4-pentanediol and 5% (w/v) inositol for 10 minutes at each step |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 16, 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: 2.3→15 Å / Num. obs: 10795 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 44.56 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.596 / Net I/av σ(I): 14.788 / Net I/σ(I): 19 / Num. measured all: 34693 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4WR9 Resolution: 2.398→14.701 Å / FOM work R set: 0.8633 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.46 / 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: 118.64 Å2 / Biso mean: 49.73 Å2 / Biso min: 22.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.398→14.701 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: 7
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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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