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Yorodumi- PDB-5muf: Crystal structure of human phosphoglycerate mutase family member ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5muf | ||||||
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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 | ||||||
Components | Serine/threonine-protein phosphatase PGAM5, mitochondrial | ||||||
Keywords | 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 | Function and homology information negative regulation of cold-induced thermogenesis / positive regulation of mitochondrial fission / myosin phosphatase activity / 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 / positive regulation of mitochondrial fission / myosin phosphatase activity / Receptor Mediated Mitophagy / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / necroptotic process / GTPase activator activity / macroautophagy / mitochondrial inner membrane / mitochondrial outer membrane / protein-containing complex binding / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: Structure / Year: 2017 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5muf.cif.gz | 258.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5muf.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 5muf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/5muf ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5muf | HTTPS FTP |
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-Related structure data
Related structure data | 3mxoSC 3o0tC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 56 - 289 / Label seq-ID: 5 - 238
NCS ensembles :
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-Components
#1: Protein | Mass: 27138.895 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM5 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 References: UniProt: Q96HS1, protein-serine/threonine phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.37 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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Refinement step | Cycle: 1 / Resolution: 3.1→41.03 Å
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Refine LS restraints |
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