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Yorodumi- PDB-1r13: Carbohydrate recognition and neck domains of surfactant protein A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r13 | ||||||
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Title | Carbohydrate recognition and neck domains of surfactant protein A (SP-A) | ||||||
Components | Pulmonary surfactant-associated protein A | ||||||
Keywords | SUGAR BINDING PROTEIN / CRD / alpha helical neck region | ||||||
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 glucocorticoid / response to retinoic acid / positive regulation of phagocytosis / multivesicular body / response to hormone / cellular response to mechanical stimulus / circadian rhythm / 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 / MAD / Resolution: 2.1 Å | ||||||
Authors | Head, J.F. / Mealy, T.R. / McCormack, F.X. / Seaton, B.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of trimeric carbohydrate recognition and neck domains of surfactant protein A Authors: Head, J.F. / Mealy, T.R. / McCormack, F.X. / 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 | 1r13.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r13.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r13_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 1r13_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 1r13_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1r13_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r13 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r13 | HTTPS FTP |
-Related 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: CRD and neck domains / Mutation: N187S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SFTPA1 OR SFTPA OR SFTP1 OR SFTP-1 / Plasmid: PVL 1392 / Genus (production host): Trichoplusia / Production host: Trichoplusia (butterflies/moths) / References: UniProt: P08427 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MES / |
#5: 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: 3.68 Å3/Da / Density % sol: 66.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: LiSO4, CaCl2, glycerol, trimannose, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 14375 / Num. obs: 14373 / % possible obs: 99.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 13.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1382 / % possible all: 98.3 |
Reflection | *PLUS Num. measured all: 189251 |
Reflection shell | *PLUS % possible obs: 98.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints | *PLUS
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