+
Open data
-
Basic information
Entry | Database: PDB / ID: 1j0c | ||||||
---|---|---|---|---|---|---|---|
Title | ACC deaminase mutated to catalytic residue | ||||||
![]() | 1-aminocyclopropane-1-carboxylate deaminase | ||||||
![]() | LYASE / PLP dependent B group | ||||||
Function / homology | ![]() amine catabolic process / 1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ose, T. / Fujino, A. / Yao, M. / Honma, M. / Tanaka, I. | ||||||
![]() | ![]() Title: Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction Authors: Ose, T. / Fujino, A. / Yao, M. / Watanabe, N. / Honma, M. / Tanaka, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 271.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 221.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 490.1 KB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j0dC ![]() 1j0eC ![]() 1f2dS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37059.047 Da / Num. of mol.: 4 / Mutation: S1A, K51T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PLP / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: ammmonium sulfate, pottasium phosphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 2002 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→38.3 Å / Num. all: 43190 / Num. obs: 43138 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 47.331 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.066 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6182 / Rsym value: 0.32 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 38 Å / Num. measured all: 241451 |
Reflection shell | *PLUS % possible obs: 99.6 % / Num. unique obs: 6182 / Num. measured obs: 35018 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F2D Resolution: 2.75→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.0438 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.85 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|