[English] 日本語
![](img/lk-miru.gif)
- PDB-5muf: Crystal structure of human phosphoglycerate mutase family member ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5muf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal WDPNWD motif | ||||||
![]() | Serine/threonine-protein phosphatase PGAM5, mitochondrial | ||||||
![]() | HYDROLASE / PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5 / PGAM5 / SERINE/THREONINE PHOSPHATASE / MITOCHONDRIAL PROTEIN / WDPNWD motif / WDXNWD motif / dimer / dodecamer / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaikuad, A. / Alfano, I. / Picaud, S. / Filippakopoulos, P. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly. Authors: Chaikuad, A. / Filippakopoulos, P. / Marcsisin, S.R. / Picaud, S. / Schroder, M. / Sekine, S. / Ichijo, H. / Engen, J.R. / Takeda, K. / Knapp, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 258.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 210.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mxoSC ![]() 3o0tC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 56 - 289 / Label seq-ID: 5 - 238
NCS ensembles :
|
-
Components
#1: Protein | Mass: 27138.895 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96HS1, protein-serine/threonine phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.37 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 18% PEG 3350 and 0.1 M MES, pH 5.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→41.03 Å / Num. obs: 18243 / % possible obs: 94.3 % / Redundancy: 7 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.101 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2 / Num. unique obs: 2709 / Rpim(I) all: 0.373 / % possible all: 96.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3MXO Resolution: 3.1→41.03 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.868 / SU B: 46.834 / SU ML: 0.369 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.597 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.1→41.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|