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Open data
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Basic information
Entry | Database: PDB / ID: 2l47 | ||||||
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Title | Solution structure of the PlyG catalytic domain | ||||||
![]() | N-acetylmuramoyl-L-alanine amidase | ||||||
![]() | HYDROLASE / Bacillus anthracis gamma-phage endolysin / PlyG / amidase-2 family / Zn-dependent peptidoglycan amidase / catalytic domain | ||||||
Function / homology | ![]() N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / peptidoglycan turnover / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / viral release from host cell by cytolysis / peptidoglycan catabolic process / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | ||||||
![]() | Volkman, B.F. / Dias, J.S. / Peterson, F.C. | ||||||
![]() | ![]() Title: Tbd Authors: Dias, J.S. / Peterson, F.C. / Volkman, B.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 930.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 18554.877 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8LTE6, N-acetylmuramoyl-L-alanine amidase |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1 mM [U-100% 13C; U-100% 15N] PlyG, 10 mM [U-99% 2H] Bis-Tris, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 13 / pH: 6 / Pressure: AMBIENT / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT Software ordinal: 1 Details: STRUCTURES ARE BASED ON A TOTAL OF 3503 NOE CONSTRAINTS (634 INTRA, 594 SEQUENTIAL, 750 MEDIUM and 1525 LONG RANGE CONSTRAINTS) AND 216 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 3503 / NOE intraresidue total count: 634 / NOE long range total count: 1525 / NOE medium range total count: 750 / NOE sequential total count: 594 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |