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- PDB-2rsc: Solution Structure of the bombyx mori lysozyme -

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Basic information

Entry
Database: PDB / ID: 2rsc
TitleSolution Structure of the bombyx mori lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / LYSOZYME
Function / homology
Function and homology information


lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBombyx mori (domestic silkworm)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsSato, M. / Tochio, N. / Aizawa, T.
CitationJournal: To be Published
Title: Solution Structure of the Bombyx Mori LYSOZYME
Authors: Sato, M. / Tochio, N. / Watanabe, S. / Kigawa, T. / Aizawa, T.
History
DepositionDec 19, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)13,8351
Polymers13,8351
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysozyme / 1 / 4-beta-N-acetylmuramidase


Mass: 13834.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P48816, lysozyme

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY

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Sample preparation

DetailsContents: 20 mM sodium acetate-1, 100 mM sodium chloride-2, 0.02 % sodium azide-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium acetate-11
100 mMsodium chloride-21
0.02 %sodium azide-31
Sample conditionsIonic strength: 120 / pH: 3.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAKobayashi, N.data analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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