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- PDB-1gbs: CRYSTAL STRUCTURE OF BLACK SWAN GOOSE-TYPE LYSOZYME AT 1.8 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 1gbs
TitleCRYSTAL STRUCTURE OF BLACK SWAN GOOSE-TYPE LYSOZYME AT 1.8 ANGSTROMS RESOLUTION
ComponentsAUSTRALIAN BLACK SWAN EGG WHITE LYSOZYME
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
Biological speciesCygnus atratus (black swan)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsRao, Z. / Machin, K. / Isaacs, N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: A strategy for rapid and effective refinement applied to black swan lysozyme.
Authors: Rao, Z. / Esnouf, R. / Isaacs, N. / Stuart, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: A Strategy for Rapid and Effective Refinement Applied to Black Swan Lysozyme
Authors: Rao, Z. / Esnouf, R. / Isaacs, N. / Stuart, D.
#2: Journal: Thesis, University of Melbourne / Year: 1989
Title: Structure Determination and Refinement of the Goose-Type Lysozyme from the Black Swan
Authors: Rao, Z.
#3: Journal: Aust.J.Biol.Sci. / Year: 1985
Title: Structure of a G-Type Goose_Type Lysozyme at 2.5 Angstroms Resolution
Authors: Isaacs, N. / Machin, K. / Masakuno, M.
History
DepositionMar 15, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AUSTRALIAN BLACK SWAN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)20,4341
Polymers20,4341
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.800, 65.400, 38.800
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 AUSTRALIAN BLACK SWAN EGG WHITE LYSOZYME


Mass: 20434.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cygnus atratus (black swan) / References: UniProt: P00717, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.83 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 19189 / % possible obs: 95 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
PROTEINrefinement
CCP4refinement
X-PLORphasing
RefinementResolution: 1.5→20 Å / σ(I): 0 /
RfactorNum. reflection% reflection
obs0.184 19189 95 %
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 0 152 1586

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