+Open data
-Basic information
Entry | Database: PDB / ID: 2yad | ||||||
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Title | BRICHOS domain of Surfactant protein C precursor protein | ||||||
Components | SURFACTANT PROTEIN C BRICHOS DOMAIN | ||||||
Keywords | SURFACTANT PROTEIN / PULMONARY SURFACTANT SYSTEM / INTERSTITIAL LUNG DISEASE / AMYLOID / CHAPERONE | ||||||
Function / homology | Function and homology information Defective pro-SFTPC causes SMDP2 and RDS / multivesicular body lumen / lamellar body / protein metabolic process => GO:0019538 / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism ...Defective pro-SFTPC causes SMDP2 and RDS / multivesicular body lumen / lamellar body / protein metabolic process => GO:0019538 / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism / endoplasmic reticulum membrane / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Askarieh, G. / Siponen, M.I. / Willander, H. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. ...Askarieh, G. / Siponen, M.I. / Willander, H. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / Jornvall, H. / Presto, J. / Johansson, J. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Nordlund, P. / Persson, C. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Berglund, H. / Knight, S.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: High Resolution Structure of a Bricos Domain and its Implications for Anti-Amyloid Chaperone Activity on Lung Surgactant Protein C. Authors: Willander, H. / Askarieh, G. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / ...Authors: Willander, H. / Askarieh, G. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / Jornvall, H. / Berglund, H. / Presto, J. / Knight, S.D. / Johansson, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yad.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yad.ent.gz | 165.7 KB | Display | PDB format |
PDBx/mmJSON format | 2yad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/2yad ftp://data.pdbj.org/pub/pdb/validation_reports/ya/2yad | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18708.883 Da / Num. of mol.: 6 / Fragment: RESIDUES 15-144 Source method: isolated from a genetically manipulated source Details: EXPRESSED N-TERMINAL SEQUENCE DIFFERS FROM UNIPROT REFERENCE Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B(DE3) / Variant (production host): PLYSS / References: UniProt: E5RI64, UniProt: P11686*PLUS #2: Water | ChemComp-HOH / | Sequence details | THE EXPRESSED PROTEIN DIFFERS FROM THE UNIPROT REFERENCE SEQUENCE AT THE N-TERMINUS. THE SEQUENCE ...THE EXPRESSED PROTEIN DIFFERS FROM THE UNIPROT REFERENCE SEQUENCE AT THE N-TERMINUS. THE SEQUENCE HMSQKHTEM IS PART OF PROTEIN AND NOT THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.32 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2010 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 34299 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 37.52 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.1 |
-Processing
Software | Name: BUSTER / Version: 2.9.2 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.2→27.43 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9078 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IN SITU PROTEOLYSIS. UNSTRUCTURED LOOP BETWEEN HELIX 1 AND HELIX 2 AS WELL AS THE N-TERMINAL S-TAG AND LINKER ARE FULLY OR PARTLY CLEAVED.
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Displacement parameters | Biso mean: 46.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.324 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→27.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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