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- PDB-2l47: Solution structure of the PlyG catalytic domain -

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Basic information

Entry
Database: PDB / ID: 2l47
TitleSolution structure of the PlyG catalytic domain
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / Bacillus anthracis gamma-phage endolysin / PlyG / amidase-2 family / Zn-dependent peptidoglycan amidase / catalytic 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
N-acetylmuramoyl-l-alanine amidase, C-terminal domain / PlyG Cell wall binding domain / : / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) 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
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6202
Polymers18,5551
Non-polymers651
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: 18554.877 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage Gamma (virus) / Gene: PlyG, GAMMALSU_0017, GAMMAUSAM_0017 / Plasmid: pBAD18 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue
References: UniProt: Q8LTE6, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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)
141

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Sample preparation

DetailsContents: 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPlyG[U-100% 13C; U-100% 15N]1
10 mMBis-Tris[U-99% 2H]1
Sample conditionsIonic strength: 13 / pH: 6 / Pressure: AMBIENT / Temperature: 303 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
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 constraintsNOE 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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