+
Open data
-
Basic information
Entry | Database: PDB / ID: 1mc1 | ||||||
---|---|---|---|---|---|---|---|
Title | BETA-LACTAM SYNTHETASE WITH PRODUCT (DGPC), AMP AND PPI | ||||||
![]() | BETA-LACTAM SYNTHETASE | ||||||
![]() | HYDROLASE / Clavulanic acid / Asparagine Synthetase / Beta-Lactam Synthetase / Carboxyethyl arginine / deoxyguanidinoproclavaminic acid | ||||||
Function / homology | ![]() (carboxyethyl)arginine beta-lactam-synthase / (carboxyethyl)arginine beta-lactam-synthase activity / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / clavulanic acid biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
![]() | ![]() Title: The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots Authors: Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 208.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 165.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 62.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m1zC ![]() 1mb9C ![]() 1mbzC ![]() 1jgtS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54601.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 415 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/PCX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/PCX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Magnesium Chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Miller, M.T., (2001) Nature Struct. Biol., 8, 684. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2000 |
Radiation | Monochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→29.1 Å / Num. all: 63373 / Num. obs: 48993 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.069 |
Reflection shell | Resolution: 2.15→2.23 Å / Rsym value: 0.293 / % possible all: 93.1 |
Reflection | *PLUS Lowest resolution: 29 Å / Num. obs: 50318 / Num. measured all: 687896 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 93.1 % / Rmerge(I) obs: 0.293 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JGT Resolution: 2.16→29.1 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.9558 Å2 / ksol: 0.385008 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.25 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→29.1 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.16→2.3 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 29 Å / % reflection Rfree: 7.8 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|