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- PDB-1hel: STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING MUTATIONS W... -

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Basic information

Entry
Database: PDB / ID: 1hel
TitleSTRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING MUTATIONS WITHIN THE CORE OF CHICKEN EGG WHITE LYSOZYME
ComponentsHEN EGG WHITE LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWilson, K.P. / Malcolm, B.A. / Matthews, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme.
Authors: Wilson, K.P. / Malcolm, B.A. / Matthews, B.W.
#1: Journal: Nature / Year: 1990
Title: Ancestral Lysozymes Reconstructed, Neutrality Tested, and Thermostability Linked to Hydrocarbon Packing
Authors: Malcolm, B.A. / Wilson, K.P. / Matthews, B.W. / Kirsch, J.F. / Wilson, A.C.
History
DepositionJan 10, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / diffrn ...atom_site / diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / pdbx_struct_special_symmetry / pdbx_validate_symm_contact / software
Item: _atom_site.occupancy / _diffrn.ambient_pressure ..._atom_site.occupancy / _diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_wavelength_list / _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf
Revision 2.1Jun 30, 2021Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_detector.detector / _diffrn_source.source
Revision 2.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.100, 79.100, 37.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

21A-318-

HOH

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Components

#1: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: EGG / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal grow
*PLUS
pH: 4.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2200 mMsodium acetate1drop
34.0 %(w/v)sodium chloride1drop
4200 mMsodium acetate1drop
54.0 %(w/v)sodium chloride1reservoir
6200 mMsodium acetate1reservoir

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Target: Cu / Voltage: 40 kV
DetectorType: OSCILLATION CAMERA / Detector: FILM / Details: Kodak No-Screen X-ray film
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
TNTrefinement
AGROVATA / ROTAVATAdata scaling
RefinementRfactor obs: 0.152 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 185 1186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.4
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
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection obs: 10276 / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 2.4

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