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Yorodumi- PDB-5oxr: Crystal structure of human lung surfactant protein D trimeric fra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oxr | |||||||||
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Title | Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R7 oligosaccharide | |||||||||
Components | Pulmonary surfactant-associated protein D | |||||||||
Keywords | SURFACTANT PROTEIN / trimeric recombinant collectin fragment / neck+CRD / alpha-helical coiled coil / carbohydrate recognition domain / lectin / sugar binding protein | |||||||||
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 / Regulation of TLR by endogenous ligand / 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 / clathrin-coated endocytic vesicle / Regulation of TLR by endogenous ligand / respiratory gaseous exchange by respiratory system / 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 / receptor-mediated endocytosis / reactive oxygen species metabolic process / 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: 1.75 Å | |||||||||
Authors | Shrive, A.K. / Greenhough, T.J. | |||||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: Structural definition of hSP-D recognition of Salmonella enterica LPS inner core oligosaccharides reveals alternative binding modes for the same LPS. Authors: Littlejohn, J.R. / da Silva, R.F. / Neale, W.A. / Smallcombe, C.C. / Clark, H.W. / Mackay, R.A. / Watson, A.S. / Madsen, J. / Hood, D.W. / Burns, I. / Greenhough, T.J. / Shrive, A.K. #1: Journal: Infect. Immun. / Year: 2016 Title: Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains. Authors: Clark, H.W. / Mackay, R.M. / Deadman, M.E. / Hood, D.W. / Madsen, J. / Moxon, E.R. / Townsend, J.P. / Reid, K.B.M. / Ahmed, A. / Shaw, A.J. / Greenhough, T.J. / Shrive, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oxr.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oxr.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 5oxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oxr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5oxr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5oxr_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5oxr_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/5oxr ftp://data.pdbj.org/pub/pdb/validation_reports/ox/5oxr | HTTPS FTP |
-Related structure data
Related structure data | 5oxsC 1pw9S 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: Trimeric neck + carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, COLEC7, PSPD, SFTP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35247 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.95 Å3/Da / Density % sol: 58.25 % / Mosaicity: 0.91 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris pH 7.0, 16% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.75→55.3 Å / Num. obs: 61250 / % possible obs: 93.2 % / Redundancy: 2.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.05 / Rrim(I) all: 0.083 / Net I/σ(I): 7.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1PW9 Resolution: 1.75→55.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.18 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0984 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.094 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.22 Å2 / Biso mean: 23.556 Å2 / Biso min: 9.69 Å2
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Refinement step | Cycle: final / Resolution: 1.75→55.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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