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- PDB-153l: THE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX WITH A B... -

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Basic information

Entry
Database: PDB / ID: 153l
TitleTHE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX WITH A BOUND TRISACCHARIDE SHOW THAT THE "GOOSE-TYPE LYSOZYMES LACK A CATALYTIC ASPARTATE
ComponentsGOOSE 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 speciesAnser anser anser (western graylag goose)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsWeaver, L.H. / Gruetter, M.G. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue.
Authors: Weaver, L.H. / Grutter, M.G. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: The Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionMay 5, 1994Processing site: BNL
Revision 1.0Jan 26, 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: GOOSE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)20,4061
Polymers20,4061
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.300, 65.700, 45.200
Angle α, β, γ (deg.)90.00, 116.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GOOSE LYSOZYME


Mass: 20406.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anser anser anser (western graylag goose)
References: UniProt: P00718, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal grow
*PLUS
pH: 6.6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium phosphate11
20.8 Msodium chloride11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 20143 / % possible obs: 73 % / Num. measured all: 71001 / Rmerge F obs: 0.074

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.6→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.15 20143
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 0 182 1614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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