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- PDB-8fol: The structure of a crystallizable variant of E. coli pyruvate for... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fol | ||||||
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Title | The structure of a crystallizable variant of E. coli pyruvate formate-lyase activating enzyme bound to SAM, alternate crystal form | ||||||
![]() | Pyruvate formate-lyase 1-activating enzyme | ||||||
![]() | OXIDOREDUCTASE / radical SAM / activase / PFL | ||||||
Function / homology | ![]() [formate-C-acetyltransferase]-activating enzyme / [formate-C-acetyltransferase]-activating enzyme activity / potassium ion binding / protein maturation / glucose metabolic process / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / DNA damage response / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Moody, J.D. / Saxton, A.J. / Galambas, A. / Lawrence, C.M. / Broderick, J.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. Authors: Moody, J.D. / Hill, S. / Lundahl, M.N. / Saxton, A.J. / Galambas, A. / Broderick, W.E. / Lawrence, C.M. / Broderick, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.3 KB | Display | ![]() |
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PDB format | ![]() | 90.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fo0C ![]() 8fsiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28237.273 Da / Num. of mol.: 1 Mutation: S1E, E53K, A93E, R111H, Q139K, E151R, K154Q, N158E, K222E, K225R, K226A, E230R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A9N4, [formate-C-acetyltransferase]-activating enzyme |
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-Non-polymers , 5 types, 16 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||
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#3: Chemical | ChemComp-SAM / | ||
#4: Chemical | ChemComp-K / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.08 % / Description: rod-like |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 4 uL of protein (10 mg/mL PFL-AE-CCR8 in 12.5 mM HEPES, 200 mM KCl, with 3.65 mM SAM, 1.2 mM WT 7-mer PFL peptide, 0.13% glycerol, and 1 mM DTT) were combined with 1 uL of crystallization ...Details: 4 uL of protein (10 mg/mL PFL-AE-CCR8 in 12.5 mM HEPES, 200 mM KCl, with 3.65 mM SAM, 1.2 mM WT 7-mer PFL peptide, 0.13% glycerol, and 1 mM DTT) were combined with 1 uL of crystallization reservoir solution (18% PEG 3350, 100 mM HEPES, pH 7.5) in hanging drop format over 50 uL of crystallization reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→35.37 Å / Num. obs: 8650 / % possible obs: 97.67 % / Redundancy: 4.3 % / Biso Wilson estimate: 55.81 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1248 / Rpim(I) all: 0.06559 / Rrim(I) all: 0.1417 / Net I/σ(I): 10.26 |
Reflection shell | Resolution: 2.65→2.745 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8407 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 752 / CC1/2: 0.71 / CC star: 0.911 / Rpim(I) all: 0.4408 / Rrim(I) all: 0.9537 / % possible all: 88.01 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→35.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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