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Yorodumi- PDB-3c3c: Crystal Structure of human phosphoglycerate kinase bound to 3-pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c3c | ||||||
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Title | Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-CDP | ||||||
Components | Phosphoglycerate kinase 1 | ||||||
Keywords | TRANSFERASE / protein-nucleotide complex / L-enantiomer of CDP / kinase / Acetylation / ATP-binding / Cytoplasm / Disease mutation / Glycolysis / Hereditary hemolytic anemia / Nucleotide-binding / Phosphoprotein / Polymorphism | ||||||
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: 2.4 Å | ||||||
Authors | Arold, S.T. / Gondeau, C. / Lionne, C. / Chaloin, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase Authors: Gondeau, C. / Chaloin, L. / Lallemand, P. / Roy, B. / Perigaud, C. / Barman, T. / Varga, A. / Vas, M. / Lionne, C. / Arold, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c3c.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c3c.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c3c ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c3c | HTTPS FTP |
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-Related structure data
Related structure data | 2zgvC 3c39C 3c3aC 3c3bC 1vjcS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44954.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)/pDIA17 / References: UniProt: P00558, phosphoglycerate kinase #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Chemical | ChemComp-CDP / | #5: 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: 2.04 Å3/Da / Density % sol: 39.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 2.6M NaKPO4, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2007 |
Radiation | Monochromator: liquid nitrogen cooled channel-cut silicon monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.6 Å / Num. all: 24806 / Num. obs: 24806 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 35.77 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2 / Num. unique all: 3617 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VJC Resolution: 2.4→43.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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