+Open data
-Basic information
Entry | Database: PDB / ID: 6h9d | ||||||
---|---|---|---|---|---|---|---|
Title | Muramidase domain of SpmX from Asticaccaulis excentricus | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / lysozyme / peptidoglycan hydrolase / cell morphogenesis / stalk synthesis | ||||||
Function / homology | Function and homology information cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / membrane => GO:0016020 / defense response to bacterium Similarity search - Function | ||||||
Biological species | Asticcacaulis excentricus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Randich, A.M. / Morlot, C.M. / Brun, Y.V. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Curr.Biol. / Year: 2019 Title: Origin of a Core Bacterial Gene via Co-option and Detoxification of a Phage Lysin. Authors: Randich, A.M. / Kysela, D.T. / Morlot, C. / Brun, Y.V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6h9d.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6h9d.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 6h9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h9d_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6h9d_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 6h9d_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6h9d_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9d ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9d | HTTPS FTP |
-Related structure data
Related structure data | 2anxS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 16667.811 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asticcacaulis excentricus (bacteria) / Gene: Astex_1112 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: E8RMG8, lysozyme #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % / Description: Large 3D needles |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5 0.2 M MgCl2 12% PEG 3350 / PH range: 8.3-8.7 |
-Data collection
Diffraction | Mean temperature: 273 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.56 Å / Num. obs: 42611 / % possible obs: 95.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.4 Å2 / Rsym value: 0.02 / Net I/σ(I): 33.99 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6805 / Rsym value: 0.436 / % possible all: 95 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ANX Resolution: 1.9→44.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.75 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.72 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→44.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|