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Yorodumi- PDB-1pwb: High resolution crystal structure of an active recombinant fragme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwb | |||||||||
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Title | High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose | |||||||||
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: 1.4 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 | 1pwb.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pwb.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pwb_validation.pdf.gz | 868.6 KB | Display | wwPDB validaton report |
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Full document | 1pwb_full_validation.pdf.gz | 872.5 KB | Display | |
Data in XML | 1pwb_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 1pwb_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwb ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwb | HTTPS FTP |
-Related structure data
Related structure data | 1pw9C 1b08S 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: 18834.957 Da / Num. of mol.: 3 / Fragment: recombinant fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P35247 #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | #3: Chemical | ChemComp-CA / #4: Sugar | #5: 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: 2.96 Å3/Da / Density % sol: 58.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 10000, Tris, maltose, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.244 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.244 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→32 Å / Num. all: 122387 / Num. obs: 122387 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.043 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.4→1.48 Å / Mean I/σ(I) obs: 3 / Num. unique all: 14247 / Rsym value: 0.245 / % possible all: 76 |
Reflection | *PLUS Num. measured all: 648490 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 76 % / Num. unique obs: 14247 / Num. measured obs: 55566 / Rmerge(I) obs: 0.245 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1b08 Resolution: 1.4→32.1 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: 1.4→32.1 Å
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LS refinement shell | Resolution: 1.4→1.46 Å
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Refinement | *PLUS Highest resolution: 1.4 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |