[English] 日本語
![](img/lk-miru.gif)
- PDB-1p0y: Crystal structure of the SET domain of LSMT bound to MeLysine and... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1p0y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy | ||||||
![]() | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast | ||||||
![]() | TRANSFERASE / SET DOMAIN / LYSINE N-METHYLATION / MULTIPLE METHYLATION / PHOTOSYNTHESIS / POST-TRANSLATIONAL MODIFICATION | ||||||
Function / homology | ![]() [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase / [fructose-bisphosphate aldolase]-lysine N-methyltransferase / [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity / protein-lysine N-methyltransferase activity / chloroplast / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Trievel, R.C. / Flynn, E.M. / Houtz, R.L. / Hurley, J.H. | ||||||
![]() | ![]() Title: Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT Authors: Trievel, R.C. / Flynn, E.M. / Houtz, R.L. / Hurley, J.H. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE AUTHORS INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE ...SEQUENCE AUTHORS INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE THAT WAS ENGINEERED INTO THE ENZYME AFTER LEU 482. AFTER CLEAVAGE, THESE SIX RESIDUES WERE LEFT ON THE C-TERMINUS OF THIS CONSTRUCT. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 287.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 230.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 61.5 KB | Display | |
Data in CIF | ![]() | 85.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ozvC ![]() 1mlvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 50629.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q43088, [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.49 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.95-1.10 M Sodium Acetate, 100 mM Methyllysine Acetate, 1 mM TCEP, 400 uM S-adenosylhomocysteine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 25, 2003 / Details: Osmic Confocal Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 84637 / Num. obs: 83829 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.044 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.55→2.64 Å / Mean I/σ(I) obs: 2.45 / Num. unique all: 7768 / Rsym value: 0.485 / % possible all: 93.6 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 93.6 % / Num. unique obs: 7768 / Rmerge(I) obs: 0.485 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MLV Resolution: 2.55→29.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 935740.33 / Data cutoff high rms absF: 935740.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.0102 Å2 / ksol: 0.345424 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→29.65 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|