+Open data
-Basic information
Entry | Database: PDB / ID: 6cnl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of H105A PGAM5 Dodecamer | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / Phosphatase / Mitophagy | ||||||
Function / homology | Function and homology information negative regulation of cold-induced thermogenesis / myosin phosphatase activity / positive regulation of mitochondrial fission / Receptor Mediated Mitophagy / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / necroptotic process / GTPase activator activity / macroautophagy ...negative regulation of cold-induced thermogenesis / myosin phosphatase activity / positive regulation of mitochondrial fission / Receptor Mediated Mitophagy / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / necroptotic process / GTPase activator activity / macroautophagy / mitochondrial outer membrane / mitochondrial inner membrane / protein-containing complex binding / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ruiz, K. / Agnew, C. / Jura, N. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Functional role of PGAM5 multimeric assemblies and their polymerization into filaments. Authors: Ruiz, K. / Thaker, T.M. / Agnew, C. / Miller-Vedam, L. / Trenker, R. / Herrera, C. / Ingaramo, M. / Toso, D. / Frost, A. / Jura, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cnl.cif.gz | 470.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cnl.ent.gz | 381.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cnl_validation.pdf.gz | 591.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6cnl_full_validation.pdf.gz | 607.2 KB | Display | |
Data in XML | 6cnl_validation.xml.gz | 78.6 KB | Display | |
Data in CIF | 6cnl_validation.cif.gz | 106.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/6cnl ftp://data.pdbj.org/pub/pdb/validation_reports/cn/6cnl | HTTPS FTP |
-Related structure data
Related structure data | 6cniC 5mufS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25407.885 Da / Num. of mol.: 12 / Mutation: H105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM5 / Production host: Escherichia coli (E. coli) References: UniProt: Q96HS1, protein-serine/threonine phosphatase #2: Protein/peptide | Mass: 1682.793 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris 7 pH, 0.2 M MgCl2 10% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.6 Å / Num. obs: 102228 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 34.72 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1983 / Rpim(I) all: 0.09759 / Rrim(I) all: 0.2219 / Net I/σ(I): 7.17 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.058 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 10012 / CC1/2: 0.565 / Rpim(I) all: 0.5104 / Rrim(I) all: 1.178 / % possible all: 99.93 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MUF Resolution: 2.6→48.6 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 27.31
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|