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- PDB-1tew: STRUCTURE OF HEXAGONAL TURKEY EGG WHITE LYSOZYME AT 1.65 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 1tew
TitleSTRUCTURE OF HEXAGONAL TURKEY EGG WHITE LYSOZYME AT 1.65 ANGSTROMS RESOLUTION
ComponentsTURKEY EGG WHITE LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


glycosaminoglycan binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / 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
THIOCYANATE ION / Lysozyme C
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsHowell, P.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of hexagonal turkey egg-white lysozyme at 1.65A resolution.
Authors: Howell, P.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: X-Ray Structure of Monoclinic Turkey Egg White Lysozyme at 1.3 Angstroms Resolution
Authors: Harata, K.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of Turkey Egg White Lysozyme Using Laue Diffraction Data
Authors: Howell, P.L. / Almo, S.C. / Parsons, M.R. / Hajdu, J. / Petsko, G.A.
History
DepositionNov 17, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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: TURKEY EGG WHITE LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2862
Polymers14,2281
Non-polymers581
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.960, 70.960, 83.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

#1: Protein TURKEY EGG WHITE LYSOZYME


Mass: 14228.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / References: UniProt: P00703, lysozyme
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMsodium acetate1drop
3150 mMpotassium thiocyanate1reservoir
450 mMsodium acetate1reservoir

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Data collection

ReflectionNum. obs: 15265 / % possible obs: 97 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 10 Å / Num. measured all: 27701 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.7 Å / % possible obs: 80 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
PROFFTrefinement
X-PLORphasing
RefinementResolution: 1.65→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.206 --
obs0.206 15112 97 %
Displacement parametersBiso mean: 23.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 3 86 1061
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.4281.5
X-RAY DIFFRACTIONx_mcangle_it2.0732
X-RAY DIFFRACTIONx_scbond_it1.6941.5
X-RAY DIFFRACTIONx_scangle_it2.5962
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.206 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.04
X-RAY DIFFRACTIONx_planar_d0.050.047
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.150.167

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