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Yorodumi- PDB-5m6z: The X-ray structure of human M189I PGK-1 mutant in partially clos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m6z | ||||||
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Title | The X-ray structure of human M189I PGK-1 mutant in partially closed conformation | ||||||
Components | Phosphoglycerate kinase 1 | ||||||
Keywords | TRANSFERASE / human phosphoglycerate kinase 1 / M189I SNP -derived mutant | ||||||
Function / homology | Function and homology information Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / ADP binding / gluconeogenesis / glycolytic process / cellular response to hypoxia / membrane raft / phosphorylation / extracellular space / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Ilari, A. / Fiorillo, A. / Petrosino, M. / Cipollone, A. | ||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme. Authors: Fiorillo, A. / Petrosino, M. / Ilari, A. / Pasquo, A. / Cipollone, A. / Maggi, M. / Chiaraluce, R. / Consalvi, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m6z.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m6z.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/5m6z ftp://data.pdbj.org/pub/pdb/validation_reports/m6/5m6z | HTTPS FTP |
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-Related structure data
Related structure data | 5m1rC 5m3uC 5mxmC 5o7dC 2zgvS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44523.387 Da / Num. of mol.: 1 / Mutation: M189I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1, PGKA, MIG10, OK/SW-cl.110 / Production host: Escherichia coli (E. coli) / References: UniProt: P00558, phosphoglycerate kinase |
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-Non-polymers , 5 types, 205 molecules
#2: Chemical | ChemComp-3PG / | ||
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#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | ChemComp-ADP / | ||
#5: Chemical | #6: 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: 2.02 Å3/Da / Density % sol: 38.51 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 2.5 M Na//KPO4, pH=8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.872899 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→60 Å / Num. obs: 42601 / % possible obs: 97.5 % / Redundancy: 4.26 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.08 |
Reflection shell | Resolution: 1.67→1.77 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.89 / CC1/2: 0.59 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZGV Resolution: 1.67→53.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.867 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / 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: 27.804 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→53.06 Å
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Refine LS restraints |
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