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Yorodumi- PDB-2ybe: The structure of the fully closed conformation of human PGK in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ybe | ||||||
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Title | The structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA aluminium tetrafluoride at 2.0 A resolution | ||||||
Components | PHOSPHOGLYCERATE KINASE 1 | ||||||
Keywords | TRANSFERASE / L-NUCLEOSIDE ANALOGUES / GLYCOLYSIS / NUCLEOTIDE BINDING | ||||||
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 / gluconeogenesis / glycolytic process / ADP binding / 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 Å | ||||||
Authors | Bowler, M.W. / Chaloin, L. / Lionne, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Interaction of Human 3-Phosphoglycerate Kinase with its Two Substrates: Is Substrate Antagonism a Kinetic Advantage? Authors: Lallemand, P. / Chaloin, L. / Roy, B. / Barman, T. / Bowler, M.W. / Lionne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ybe.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ybe.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 2ybe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2ybe ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2ybe | HTTPS FTP |
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-Related structure data
Related structure data | 2y3iC 2wzcS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44672.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00558, phosphoglycerate kinase |
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-Non-polymers , 6 types, 121 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-LA8 / |
#5: Chemical | ChemComp-ALF / |
#6: Chemical | ChemComp-3PG / |
#7: Water | ChemComp-HOH / |
-Details
Nonpolymer details | ADENOSINE-5'-DIPHOSPHAT |
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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: 2.29 Å3/Da / Density % sol: 46.33 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 29% PEG 2000MME, 0.1 M BIS/TRIS PH 6.25 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.932 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2011 / Details: GE 221 |
Radiation | Monochromator: DIAMOND 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.7 Å / Num. obs: 25350 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WZC Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.603 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.186 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.468 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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