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- PDB-1e8l: NMR solution structure of hen lysozyme -

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Basic information

Entry
Database: PDB / ID: 1e8l
TitleNMR solution structure of hen lysozyme
ComponentsLYSOZYME
KeywordsHYDROLASE
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
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 speciesGALLUS GALLUS (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsSchwalbe, H. / Grimshaw, S.B. / Spencer, A. / Buck, M. / Boyd, J. / Dobson, C.M. / Redfield, C. / Smith, L.J.
CitationJournal: Protein Sci. / Year: 2001
Title: A refined solution structure of hen lysozyme determined using residual dipolar coupling data.
Authors: Schwalbe, H. / Grimshaw, S.B. / Spencer, A. / Buck, M. / Boyd, J. / Dobson, C.M. / Redfield, C. / Smith, L.J.
History
DepositionSep 27, 2000Deposition site: PDBE / Processing site: PDBE
SupersessionOct 9, 2000ID: 1HWA
Revision 1.0Oct 9, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)14,3311
Polymers14,3311
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)50 / 300LOWEST ENERGY
RepresentativeModel #49

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Components

#1: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Cellular location: EGG WHITE / Production host: ASPERGILLUS NIGER (mold) / Strain (production host): TRANSFORMANT B1 / References: UniProt: P00698, lysozyme
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HNCO
131(H)CCH-TOCSY
14113C NOESY-HMQC
151(H)CCH-COSY
16115N NOESY-HMQC
171HMQCJ
181(H)CCH-E.COSY
19115N HSQC
NMR detailsText: NOE DATA FROM EXPERIMENTS ON 13C,15N-LABELED SAMPLE. STRUCTURES REFINED USING 209 RESIDUAL 1H-15N DIPOLAR COUPLING RESTRAINTS FROM MEASUREMENTS MADE IN TWO DIFFERENT LIQUID CRYSTALLINE PHASES.

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Sample preparation

Sample conditionspH: 3.8 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built home builtHome-builthome built5001
Home-built home builtHome-builthome built6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: DETAILS OF THE NMR DATA USED IN THE STRUCTURE CALCULATIONS ARE AS FOLLOWS NUMBER OF RESTRAINTS NOE DISTANCE RESTRAINTS 1632 HYDROGEN BOND RESTRAINTS 60 DIHEDRAL ANGLE PHI RESTRAINTS 51 ...Details: DETAILS OF THE NMR DATA USED IN THE STRUCTURE CALCULATIONS ARE AS FOLLOWS NUMBER OF RESTRAINTS NOE DISTANCE RESTRAINTS 1632 HYDROGEN BOND RESTRAINTS 60 DIHEDRAL ANGLE PHI RESTRAINTS 51 DIHEDRAL ANGLE CHI 1 RESTRAINTS 59 RESIDUAL DIPOLAR COUPLING RESTRAINTS 209 RMS DEVIATIONS FROM EXPERIMENTAL RESTRAINTS NOE RESTRAINTS (ANGSTROMS) 0.0439 DIHEDRAL RESTRAINTS (DEGREES) 0.655 DIPOLAR COUPLING RESTRAINTS (HZ) 1.159 RMS DEVIATIONS FROM IDEAL COVALENT GEOMETRY BONDS (ANGSTROMS) 0.00333 ANGLES (DEGREES) 0.492 IMPROPERS (DEGREES) 0.384
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 300 / Conformers submitted total number: 50

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