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- PDB-154l: THE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX WITH A B... -

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Basic information

Entry
Database: PDB / ID: 154l
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 / homologyTransglycosylase SLT domain 1 / Glycoside hydrolase, family 23 / Lysozyme-like domain superfamily / Transglycosylase SLT domain / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cytolysis / defense response to bacterium ...Transglycosylase SLT domain 1 / Glycoside hydrolase, family 23 / Lysozyme-like domain superfamily / Transglycosylase SLT domain / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cytolysis / defense response to bacterium / extracellular region / Lysozyme g
Function and homology information
MethodX-RAY DIFFRACTION / 1.6 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 5, 1994 / Release: Jan 26, 1995
RevisionDateData content typeGroupProviderType
1.0Jan 26, 1995Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GOOSE LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0704
Polyers20,4061
Non-polymers6643
Water2,954164
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)38.300, 65.400, 44.700
Angle α, β, γ (deg.)90.00, 117.00, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide GOOSE LYSOZYME


Mass: 20406.139 Da / Num. of mol.: 1 / References: UniProt: P00718, lysozyme
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 3 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 / Density percent sol: 49.67 %
Crystal grow
*PLUS
pH: 6.6 / Method: batch method
components of the solutions
*PLUS
IDConcCommon 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
D resolution high: 1.6 Å / Number obs: 21303 / Number measured all: 72401 / Percent possible obs: 74 / Rmerge F obs: 0.074

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Processing

SoftwareName: TNT / Classification: refinement
RefineSigma F: 0
Least-squares processR factor obs: 0.159 / Highest resolution: 1.6 Å / Lowest resolution: 6 Å / Number reflection obs: 21303
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 1432 / Nucleic acid: 0 / Ligand: 43 / Solvent: 164 / Total: 1639
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.5
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
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.159
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 2.5

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