+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h18 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Pyruvate Formate-Lyase (E.coli) in complex with Pyruvate | |||||||||
![]() | FORMATE ACETYLTRANSFERASE 1 | |||||||||
![]() | TRANSFERASE / LYASE / GLYCYL RADICAL ENZYME / ACYLTRANSFERASE / ACETYLATION | |||||||||
Function / homology | ![]() formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Becker, A. / Kabsch, W. | |||||||||
![]() | ![]() Title: X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical for Pyruvate Cleavage Authors: Becker, A. / Kabsch, W. | |||||||||
History |
| |||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 340.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 277.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1h16C ![]() 1h17C ![]() 3pflS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 85327.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: COMPLEX OF PYRUVATE FORMATE-LYASE WITH ITS SUBSTRATE PYRUVATE Source: (natural) ![]() ![]() |
---|
-Non-polymers , 5 types, 1225 molecules ![](data/chem/img/PYR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-DTL / #5: Chemical | ChemComp-PG4 / #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | GLUCOSE NONOXIDATI |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.42 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.3 / Details: pH 7.30 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 98536 / % possible obs: 94.9 % / Redundancy: 9.83 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.66 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.39 / % possible all: 92.6 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 86674 / % possible obs: 95.2 % / Num. measured all: 908602 / Rmerge(I) obs: 0.122 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 92.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PFL Resolution: 2.3→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 5224229.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.5313 Å2 / ksol: 0.32319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|