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Yorodumi- PDB-1pw9: High resolution crystal structure of an active recombinant fragme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pw9 | ||||||
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Title | High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D | ||||||
Components | Pulmonary surfactant-associated protein D | ||||||
Keywords | SIGNALING PROTEIN / collectin / c-type lectin / alpha-helical coiled-coil / carbohydrate recognition domain | ||||||
Function / homology | Function and homology information Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / negative regulation of interleukin-2 production / lung alveolus development / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / reactive oxygen species metabolic process / receptor-mediated endocytosis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / SARS-CoV-1 activates/modulates innate immune responses / carbohydrate binding / lysosome / defense response to bacterium / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Shrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B. / Greenhough, T.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: High resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D Authors: Shrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B. / Greenhough, T.J. #1: Journal: Structure / Year: 1999 Title: Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D Authors: Hakansson, K. / Lim, N.K. / Hoppe, H.J. / Reid, K.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pw9.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pw9.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 1pw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pw9 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pw9 | HTTPS FTP |
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-Related structure data
Related structure data | 1pwbSC 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: 18834.957 Da / Num. of mol.: 3 / Fragment: Residues 179-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, SFTP4, PSPD / Production host: Escherichia coli (E. coli) / References: UniProt: P35247 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 4000, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2001 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→56 Å / Num. all: 84773 / Num. obs: 84773 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.054 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 11823 / Rsym value: 0.167 / % possible all: 93.3 |
Reflection | *PLUS Num. measured all: 236479 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 93.3 % / Num. unique obs: 11823 / Num. measured obs: 22539 / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1pwb Resolution: 1.6→55.5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→55.5 Å
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LS refinement shell | Resolution: 1.6→1.67 Å /
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Refinement | *PLUS Highest resolution: 1.6 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |