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Open data
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Basic information
Entry | Database: PDB / ID: 6h9d | ||||||
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Title | Muramidase domain of SpmX from Asticaccaulis excentricus | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / lysozyme / peptidoglycan hydrolase / cell morphogenesis / stalk synthesis | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Randich, A.M. / Morlot, C.M. / Brun, Y.V. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.1 KB | Display | ![]() |
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PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 457.8 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2anxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 16667.811 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % / Description: Large 3D needles |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: 1 / Resolution: 1.9→44.56 Å
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Refine LS restraints |
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