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Yorodumi- PDB-2ggx: Crystal structure of the trimer neck and carbohydrate recognition... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ggx | ||||||
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Title | Crystal structure of the trimer neck and carbohydrate recognition domain of human surfactant protein D in complex with p-nitrophenyl maltoside | ||||||
Components | Pulmonary surfactant-associated protein D | ||||||
Keywords | SUGAR BINDING PROTEIN / protein-carbohydrate ligand complex | ||||||
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: 1.9 Å | ||||||
Authors | Head, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Contributions of Phenylalanine 335 to Ligand Recognition by Human Surfactant Protein D: ring interactions with Sp-D ligands Authors: Crouch, E. / McDonald, B. / Smith, K. / Cafarella, T. / Seaton, B. / Head, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ggx.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ggx.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ggx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2ggx ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2ggx | HTTPS FTP |
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-Related structure data
Related structure data | 2gguC 1pwbS 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: 17272.209 Da / Num. of mol.: 3 / Fragment: Trimeric neck and carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD / Plasmid: pET-30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Blue / References: UniProt: P35247 #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 8000, 150mM NaCl, 10mM CaCl2, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 50803 / Num. obs: 50803 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Χ2: 1.4 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.287 / Num. unique obs: 5121 / Χ2: 1.646 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1pwb Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 43.099 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.232 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å /
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Xplor file |
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