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Yorodumi- PDB-1ccd: REFINED STRUCTURE OF RAT CLARA CELL 17 KDA PROTEIN AT 3.0 ANGSTRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ccd | ||||||
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Title | REFINED STRUCTURE OF RAT CLARA CELL 17 KDA PROTEIN AT 3.0 ANGSTROMS RESOLUTION | ||||||
Components | CLARA CELL 17 kD PROTEIN | ||||||
Keywords | PHOSPHOLIPASE A2 INHIBITOR | ||||||
Function / homology | Function and homology information polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / response to silicon dioxide / phospholipase A2 inhibitor activity / response to ozone / response to fibroblast growth factor / : / negative regulation of type II interferon production ...polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / response to silicon dioxide / phospholipase A2 inhibitor activity / response to ozone / response to fibroblast growth factor / : / negative regulation of type II interferon production / negative regulation of T cell proliferation / T cell proliferation / response to glucocorticoid / regulation of mRNA stability / secretory granule / response to cytokine / nuclear envelope / regulation of inflammatory response / response to lipopolysaccharide / response to xenobiotic stimulus / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Umland, T.C. / Swaminathan, S. / Furey, W. / Singh, G. / Pletcher, J. / Sax, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Refined structure of rat Clara cell 17 kDa protein at 3.0 A resolution. Authors: Umland, T.C. / Swaminathan, S. / Furey, W. / Singh, G. / Pletcher, J. / Sax, M. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization and Preliminary X-Ray Study of Rat Clara Cell 10,000 MR Protein Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Katyal, S. / Singh, G. / Sax, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ccd.cif.gz | 24.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ccd.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ccd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ccd_validation.pdf.gz | 424.5 KB | Display | wwPDB validaton report |
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Full document | 1ccd_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 1ccd_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1ccd_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/1ccd ftp://data.pdbj.org/pub/pdb/validation_reports/cc/1ccd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8475.677 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P17559 |
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#2: Chemical | ChemComp-SO4 / |
Compound details | THE AMINO ACID SEQUENCE OF RAT CLARA CELL 17 KDA PROTEIN IS 55.7 PERCENT IDENTICAL TO THAT OF ...THE AMINO ACID SEQUENCE OF RAT CLARA CELL 17 KDA PROTEIN IS 55.7 PERCENT IDENTICAL TO THAT OF RABBIT UTEROGLOBI |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.1 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 9999 Å / Num. obs: 1733 / % possible obs: 85 % / Rmerge(I) obs: 2 / Rmerge F obs: 0.117 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.4 Å / % possible obs: 63.3 % / Num. unique obs: 381 / Num. measured obs: 602 |
-Processing
Software |
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Refinement | Rfactor obs: 0.225 / Highest resolution: 3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 1661 / Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 7.23 Å2 |