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Yorodumi- PDB-2ork: crystal structure of the trimeric neck and carbohydrate recogniti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ork | ||||||
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Title | crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with inositol-1-phosphate | ||||||
Components | Pulmonary surfactant-associated protein D | ||||||
Keywords | SUGAR BINDING PROTEIN / Surfactant protein / Carbohydrate recognition domain / trimeric | ||||||
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 / Regulation of TLR by endogenous ligand / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / 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 / Regulation of TLR by endogenous ligand / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / lung alveolus development / negative regulation of interleukin-2 production / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / receptor-mediated endocytosis / reactive oxygen species metabolic process / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / FOURIER SYNTHESIS / Resolution: 1.89 Å | ||||||
Authors | Head, J.F. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Critical Role of Arg/Lys343 in the Species-Dependent Recognition of Phosphatidylinositol by Pulmonary Surfactant Protein D. Authors: Crouch, E. / McDonald, B. / Smith, K. / Roberts, M. / Mealy, 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 | 2ork.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ork.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ork.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ork_validation.pdf.gz | 795.6 KB | Display | wwPDB validaton report |
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Full document | 2ork_full_validation.pdf.gz | 797.7 KB | Display | |
Data in XML | 2ork_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 2ork_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/2ork ftp://data.pdbj.org/pub/pdb/validation_reports/or/2ork | HTTPS FTP |
-Related structure data
Related structure data | 2orjC 2os9C 2gguS 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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Details | The single trimer of head and neck domains present in the asymmetric unit is the functional unit. |
-Components
#1: Protein | Mass: 17272.209 Da / Num. of mol.: 3 / Fragment: head and neck domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, PSPD, SFTP4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettablue / 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: 3.21 Å3/Da / Density % sol: 61.72 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 150mM NaCl, 10mM CaCl2, 12% PEG 8000, 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: Jul 29, 2006 |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.66 Å / Num. all: 51917 / Num. obs: 48123 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 46.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 17 / Num. unique all: 3737 / Rsym value: 0.067 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2GGU Resolution: 1.89→38.66 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / SU B: 2.402 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.249 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.94 Å / Total num. of bins used: 20
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