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Open data
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Basic information
Entry | Database: PDB / ID: 2b0p | ||||||
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Title | truncated S. aureus LytM, P212121 crystal form | ||||||
![]() | Glycyl-glycine endopeptidase lytM | ||||||
![]() | HYDROLASE / LytM / lysostaphin / peptidoglycan amidase / peptidase | ||||||
Function / homology | ![]() lysostaphin / septum digestion after cytokinesis / peptide catabolic process / cobalt ion binding / cell division site / nickel cation binding / cell outer membrane / cell wall organization / metalloendopeptidase activity / manganese ion binding ...lysostaphin / septum digestion after cytokinesis / peptide catabolic process / cobalt ion binding / cell division site / nickel cation binding / cell outer membrane / cell wall organization / metalloendopeptidase activity / manganese ion binding / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Firczuk, M. / Mucha, A. / Bochtler, M. | ||||||
![]() | ![]() Title: Crystal structures of active LytM. Authors: Firczuk, M. / Mucha, A. / Bochtler, M. #1: ![]() Title: Latent LytM at 1.3A resolution. Authors: Odintsov, S.G. / Sabala, I. / Marcyjaniak, M. / Bochtler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b13C ![]() 2b44C ![]() 1qwyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14564.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 0.1 M sodium acetate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 42130 / Num. obs: 42130 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6060 / Rsym value: 0.256 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QWY Resolution: 1.5→19.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.205 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.184 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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