+Open data
-Basic information
Entry | Database: PDB / ID: 4m67 | ||||||
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Title | Crystal structure of the human MLKL kinase-like domain | ||||||
Components | Mixed lineage kinase domain-like protein | ||||||
Keywords | SIGNALING PROTEIN / kinase-like / a substrate of RIP3 / RIP3 | ||||||
Function / homology | Function and homology information execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / necroptotic process / protein homotrimerization / Regulation of necroptotic cell death / cell junction / defense response to virus ...execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / necroptotic process / protein homotrimerization / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Xie, T. / Peng, W. / Yan, C. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: Cell Rep / Year: 2013 Title: Structural Insights into RIP3-Mediated Necroptotic Signaling Authors: Xie, T. / Peng, W. / Yan, C. / Wu, J. / Gong, X. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m67.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m67.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 4m67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m67_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 4m67_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 4m67_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4m67_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/4m67 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/4m67 | HTTPS FTP |
-Related structure data
Related structure data | 4m66C 4m68C 4m69C 4ithS 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: 33634.895 Da / Num. of mol.: 1 / Fragment: UNP residues 179-471 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NB16 |
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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: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 13% PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 6, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 27321 / Num. obs: 27185 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 29.54 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ITH Resolution: 1.9→37.56 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8429 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.566 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.75 Å2 / Biso mean: 33.9892 Å2 / Biso min: 14.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.56 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -18.2874 Å / Origin y: -4.9954 Å / Origin z: -16.2714 Å
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Refinement TLS group | Selection details: ALL |