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- PDB-4rh3: AMPPCP-bound structure of human platelet phosphofructokinase in a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rh3 | ||||||
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Title | AMPPCP-bound structure of human platelet phosphofructokinase in an R-state, crystal form II | ||||||
![]() | ATP-dependent 6-phosphofructokinase, platelet type | ||||||
![]() | TRANSFERASE / Phosphohexokinase | ||||||
Function / homology | ![]() 6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / Glycolysis / AMP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / Glycolysis / AMP binding / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kloos, M. | ||||||
![]() | ![]() Title: Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation. Authors: Kloos, M. / Bruser, A. / Kirchberger, J. / Schoneberg, T. / Strater, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 925.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 97.6 KB | Display | |
Data in CIF | ![]() | 131.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 25 - 762 / Label seq-ID: 6 - 743
NCS ensembles :
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Components
#1: Protein | Mass: 81111.844 Da / Num. of mol.: 4 / Fragment: UNP residues 26-762 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ACP / #3: Chemical | ChemComp-PO4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0,1 M MES pH 6.0 23% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2014 | |||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.02→50 Å / Num. obs: 80705 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.184 / Net I/σ(I): 12.32 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: 4WLO / Resolution: 3.02→46.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.558 / SU ML: 0.154 / SU R Cruickshank DPI: 0.0545 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / 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: 78.049 Å2
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Refinement step | Cycle: LAST / Resolution: 3.02→46.9 Å
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Refine LS restraints |
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