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Yorodumi- PDB-3pbf: Surfactant Protein-A neck and carbohydrate recognition domain (NC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pbf | ||||||
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Title | Surfactant Protein-A neck and carbohydrate recognition domain (NCRD) complexed with glycerol | ||||||
Components | Pulmonary surfactant-associated protein A | ||||||
Keywords | SUGAR BINDING PROTEIN / collectin / carbohydrate binding / lectin / mannose | ||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Shang, F. / Rynkiewicz, M.J. / McCormack, F.X. / Wu, H. / Cafarella, T.M. / Head, J. / Seaton, B.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystallographic complexes of surfactant protein A and carbohydrates reveal ligand-induced conformational change. Authors: Shang, F. / Rynkiewicz, M.J. / McCormack, F.X. / Wu, H. / Cafarella, T.M. / Head, J.F. / Seaton, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pbf.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pbf.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pbf_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 3pbf_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 3pbf_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3pbf_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/3pbf ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pbf | HTTPS FTP |
-Related structure data
Related structure data | 3pakC 3paqC 3parC 1r13S 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: 16672.580 Da / Num. of mol.: 1 / Fragment: UNP residues 101-248 / Mutation: N187S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sftp-1, Sftp1, Sftpa, Sftpa1 / Plasmid: PVL 1392 / Production host: TRICHOPLUSIA (butterflies/moths) / References: UniProt: P08427 | ||
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#2: Chemical | ChemComp-CA / | ||
#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: 3.69 Å3/Da / Density % sol: 66.63 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1ul SP-A (10 mg/ml) was mixed with 1ul reservoir (50 mM sodium cacodylate (pH = 6.5), 1.2-1.6 M lithium sulfate, 10 mM calcium chloride, and 5 % v/v glycerol. Prior to data collection, ...Details: 1ul SP-A (10 mg/ml) was mixed with 1ul reservoir (50 mM sodium cacodylate (pH = 6.5), 1.2-1.6 M lithium sulfate, 10 mM calcium chloride, and 5 % v/v glycerol. Prior to data collection, crystals were cryoprotected in a solution with higher amounts of glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 15, 2002 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 22680 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2206 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB CODE 1R13 Resolution: 1.8→23.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 545437.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.3681 Å2 / ksol: 0.376265 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→23.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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