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- PDB-1lsp: THE CRYSTAL STRUCTURE OF A BULGECIN-INHIBITED G-TYPE LYSOZYME FRO... -

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Basic information

Entry
Database: PDB / ID: 1lsp
TitleTHE CRYSTAL STRUCTURE OF A BULGECIN-INHIBITED G-TYPE LYSOZYME FROM THE EGG-WHITE OF THE AUSTRALIAN BLACK SWAN. A COMPARISON OF THE BINDING OF BULGECIN TO THREE MURAMIDASES
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Glycoside hydrolase, family 23 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BULGECIN A / Lysozyme g
Similarity search - Component
Biological speciesCygnus atratus (black swan)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsKarlsen, S. / Rao, Z.H. / Hough, E. / Isaacs, N.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of a bulgecin-inhibited g-type lysozyme from the egg white of the Australian black swan. A comparison of the binding of bulgecin to three muramidases.
Authors: Karlsen, S. / Hough, E. / Rao, Z.H. / Isaacs, N.W.
#1: Journal: To be Published
Title: The Crystal Structure of a Complex between Bulgecin, a Bacterial Metabolite, and Lysozyme from the Rainbow Trout
Authors: Karlsen, S. / Hough, E.
#2: Journal: Aust.J.Biol.Sci. / Year: 1985
Title: Three-Dimensional Structure of Goose-Type Lysozyme from the Egg White of the Australian Black Swan, Cygnus Atratus
Authors: Isaacs, N.W. / Machin, K.J. / Masakuni, M.
#3: Journal: Tetrahedron / Year: 1984
Title: Structures of Bulgecins, Bacterial Metabolites with Bulge-Inducing Activity
Authors: Shinagawa, S. / Kasahara, F. / Wada, Y. / Harada, S. / Asai, M.
History
DepositionFeb 9, 1995Processing site: BNL
Revision 1.0Jan 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 19, 2014Group: Other
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9862
Polymers20,4341
Non-polymers5521
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.690, 65.330, 38.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein LYSOZYME / MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE


Mass: 20434.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cygnus atratus (black swan) / Cellular location: EGG WHITE / References: UniProt: P00717, lysozyme
#2: Chemical ChemComp-BUL / BULGECIN A


Mass: 551.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H29N3O14S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.99 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
225 %(w/v)11NaCl
1phosphate11

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 6959 / % possible obs: 78.9 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 32.94 Å

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Processing

Software
NameClassification
XDSdata scaling
PROLSQrefinement
XDSdata reduction
RefinementResolution: 2.45→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.175 6959
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 35 109 1578
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0530.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0730.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.0450.06
X-RAY DIFFRACTIONp_singtor_nbd0.2240.03
X-RAY DIFFRACTIONp_multtor_nbd0.2760.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2240.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.9293
X-RAY DIFFRACTIONp_staggered_tor22.68715
X-RAY DIFFRACTIONp_orthonormal_tor29.12320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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