+
Open data
-
Basic information
Entry | Database: PDB / ID: 5lhm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of SafC from Myxococcus xanthus apo-Form | ||||||
![]() | Putative O-methyltransferase | ||||||
![]() | TRANSFERASE / O-METHYL TRANSFERASE / SAM | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gerhardt, S. / Netzer, J. / Einsle, O. | ||||||
![]() | ![]() Title: Functional and structural characterisation of a bacterial O-methyltransferase and factors determining regioselectivity. Authors: Siegrist, J. / Netzer, J. / Mordhorst, S. / Karst, L. / Gerhardt, S. / Einsle, O. / Richter, M. / Andexer, J.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.8 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5logC ![]() 2hnkS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26262.963 Da / Num. of mol.: 1 / Mutation: A77T Source method: isolated from a genetically manipulated source Details: Mutation A77T / Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-BU3 / ( #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % / Mosaicity: 0.14 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG MME 5000, Sodium Acetate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 31, 2014 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→118.16 Å / Num. obs: 69174 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 13.71 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.144 / Rsym value: 0.152 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.311→1.38 Å / Redundancy: 20.3 % / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.405 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2HNK Resolution: 1.31→19.18 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.045 / SU Rfree Cruickshank DPI: 0.044
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.39 Å2 / Biso mean: 20.01 Å2 / Biso min: 7.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.31→19.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.31→1.34 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -24.1514 Å / Origin y: 11.6635 Å / Origin z: -12.7711 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |