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- PDB-2l48: Solution structure of the PlyG cell wall binding domain -

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Basic information

Entry
Database: PDB / ID: 2l48
TitleSolution structure of the PlyG cell wall binding domain
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsCarbohydrate-Binding Protein / Bacillus anthracis gamma- phage endolysin / PlyG / cell wall binding domain / homodimer / ACT-type domain
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / sporulation resulting in formation of a cellular spore / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall organization / defense response to bacterium
Similarity search - Function
Alpha-Beta Plaits - #2030 / N-acetylmuramoyl-l-alanine amidase, C-terminal domain / PlyG Cell wall binding domain / : / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesBacillus phage Gamma (virus)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Dias, J.S. / Peterson, F.C.
CitationJournal: To be Published
Title: Tbd
Authors: Dias, J.S. / Peterson, F.C. / Volkman, B.F.
History
DepositionOct 1, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase
B: N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)18,8952
Polymers18,8952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase


Mass: 9447.730 Da / Num. of mol.: 2 / Fragment: cell wall binding domain, residues 151-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage Gamma (virus) / Gene: GAMMALSU_0017, GAMMAUSAM_0017, PlyG / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[pREP4] / References: UniProt: Q8LTE6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 1.25 mM [U-100% 13C; U-100% 15N] PlyG, 20 mM [U-99% 2H] Bis-Tris, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMPlyG[U-100% 13C; U-100% 15N]1
20 mMBis-Tris[U-99% 2H]1
Sample conditionsIonic strength: 13 / pH: 6 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE ...Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, 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: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 3966 NOE CONSTRAINTS (704 INTRA, 726 SEQUENTIAL, 958 MEDIUM and 1442 INTRAMONOMER LONG RANGE AND 136 INTERMONOMER CONSTRAINTS) AND 220 PHI AND ...Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 3966 NOE CONSTRAINTS (704 INTRA, 726 SEQUENTIAL, 958 MEDIUM and 1442 INTRAMONOMER LONG RANGE AND 136 INTERMONOMER CONSTRAINTS) AND 220 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINTS WERE ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATD TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND MONOMER. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONTRAINTS FROM BOTH MONOMERS, HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 3966 NOE CONSTRAINTS (704 INTRA, 726 SEQUENTIAL, 958 MEDIUM and 1422 INTRAMONOMER LONG RANGE AND 136 INTERMONOMER CONSTRAINTS) AND 220 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINTS WERE ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATD TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND MONOMER. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONTRAINTS FROM BOTH MONOMERS
NMR constraintsNOE constraints total: 3966 / NOE intraresidue total count: 704 / NOE long range total count: 1578 / NOE medium range total count: 958 / NOE sequential total count: 726
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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