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Yorodumi- PDB-4n1l: Crystal structures of NLRP14 pyrin domain reveal a conformational... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n1l | ||||||
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Title | Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions | ||||||
Components | NACHT, LRR and PYD domains-containing protein 14 | ||||||
Keywords | SIGNALING PROTEIN / death domain fold / pyrin domain / NOD-like receptor / protein binding / spermatogenesis / innate immunity | ||||||
Function / homology | Function and homology information regulation of inflammatory response / spermatogenesis / cell differentiation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.986 Å | ||||||
Authors | Eibl, C. / Hessenberger, M. / Wenger, J. / Brandstetter, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions. Authors: Eibl, C. / Hessenberger, M. / Wenger, J. / Brandstetter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n1l.cif.gz | 32.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n1l.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n1l_validation.pdf.gz | 411.3 KB | Display | wwPDB validaton report |
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Full document | 4n1l_full_validation.pdf.gz | 411.3 KB | Display | |
Data in XML | 4n1l_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 4n1l_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/4n1l ftp://data.pdbj.org/pub/pdb/validation_reports/n1/4n1l | HTTPS FTP |
-Related 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: 12309.033 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100 / Mutation: L84R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP14, NALP14, NOD5 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Star (DE3) / References: UniProt: Q86W24 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Ammonium acetate and 2.2 M Ammonium sulfate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2012 / Details: mirrors |
Radiation | Monochromator: horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.986→39.72 Å / Num. obs: 6916 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % |
Reflection shell | Resolution: 1.986→2.09 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NLRP14 PYD Ser6-Pro67 Resolution: 1.986→39.689 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 22.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.986→39.689 Å
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Refine LS restraints |
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LS refinement shell |
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