[English] 日本語
![](img/lk-miru.gif)
- PDB-5dmn: Crystal Structure of the Homocysteine Methyltransferase MmuM from... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5dmn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli, Apo form | |||||||||
![]() | Homocysteine S-methyltransferase | |||||||||
![]() | TRANSFERASE / Homocysteine Methyltransferase | |||||||||
Function / homology | ![]() homocysteine S-methyltransferase / S-adenosylmethionine-homocysteine S-methyltransferase activity / S-methylmethionine metabolic process / S-methylmethionine cycle / S-methylmethionine-homocysteine S-methyltransferase activity / methionine biosynthetic process / methylation / DNA damage response / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, K. / Li, G. / Bradbury, L.M.T. / Andrew, H.D. / Bruner, S.D. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli. Authors: Li, K. / Li, G. / Bradbury, L.M. / Hanson, A.D. / Bruner, S.D. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dmlC ![]() 5dmmC ![]() 1q7mS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33457.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: mmuM, yagD, b0261, JW0253 / Production host: ![]() ![]() References: UniProt: Q47690, homocysteine S-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % / Description: rod-shape |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.6 M ammonium sulfate, 10% v/v glycerol and 0.1 M sodium acetate, pH 4.8 PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2015 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.892→38.425 Å / Num. obs: 13530 / % possible obs: 99.71 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.151 / Rsym value: 0.165 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 2.892→2.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.54 / % possible all: 98.41 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1Q7M Resolution: 2.892→38.425 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.16 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.892→38.425 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|