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- PDB-3zoz: The structure of human phosphoglycerate kinase with bound bromide... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zoz | ||||||
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Title | The structure of human phosphoglycerate kinase with bound bromide, a stimulating anion. | ||||||
![]() | PHOSPHOGLYCERATE KINASE 1 | ||||||
![]() | TRANSFERASE / PHOSPHORYL TRANSFER / ANION STIMULATION / ALLOSTERIC | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bowler, M.W. | ||||||
![]() | ![]() Title: Identification of the Activating Anion Binding Site in Human Phosphoglycerate Kinase Authors: Bowler, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.6 KB | Display | ![]() |
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PDB format | ![]() | 75.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 757.5 KB | Display | ![]() |
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Full document | ![]() | 758.7 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wzcS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 436 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/MGF.gif)
![](data/chem/img/3PG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/MGF.gif)
![](data/chem/img/3PG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-BR / |
#4: Chemical | ChemComp-MGF / |
#5: Chemical | ChemComp-3PG / |
#6: Chemical | ChemComp-ADP / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 35% PEG2000MME, 0.1M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 24, 2009 / Details: MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→54 Å / Num. obs: 29204 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 7 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WZC Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.144 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.148 / 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: 17.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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