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- PDB-5xz7: Crystal Structure of Phosphofructokinase from Staphylococcus aure... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xz7 | ||||||
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Title | Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue | ||||||
![]() | ATP-dependent 6-phosphofructokinase | ||||||
![]() | TRANSFERASE / Phosphofructokinase / Staphylococcus aureus | ||||||
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 / AMP binding / ATP 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 / AMP binding / ATP binding / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C.L. / Tian, T. / Zang, J.Y. | ||||||
![]() | ![]() Title: Structural Insights into the Regulation of Staphylococcus aureus Phosphofructokinase by Tetramer-Dimer Conversion. Authors: Tian, T. / Wang, C.L. / Wu, M.H. / Zhang, X. / Zang, J.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.5 KB | Display | ![]() |
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PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.9 KB | Display | ![]() |
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Full document | ![]() | 813.1 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xoeSC ![]() 5xz6C ![]() 5xz8C ![]() 5xz9C ![]() 5xzaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35954.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 8325 / Gene: pfkA, SAOUHSC_01807 / Production host: ![]() ![]() References: UniProt: Q2FXM8, UniProt: P99165*PLUS, 6-phosphofructokinase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Sugar | ChemComp-F6P / | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.95 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 15% PEG4000, 0.1M MES PH 6.0 , 0.15M(NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→66.9 Å / Num. obs: 47521 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 6845 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XOE Resolution: 1.6→66.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.255 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.072 / 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: 15.544 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→66.9 Å
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Refine LS restraints |
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