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- PDB-1kxw: ANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPO... -

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Basic information

Entry
Database: PDB / ID: 1kxw
TitleANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPOLE AND CHARGED SIDE CHAINS
ComponentsLYSOZYME
KeywordsHYDROLASE / GLYCOSIDASE / ELECTROSTATIC INTERACTION / HELIX / HEN LYSOZYME / STABILITY
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: 1.96 Å
AuthorsMotoshima, H. / Ohmura, T. / Ueda, T. / Imoto, T.
CitationJournal: J.Biochem.(Tokyo) / Year: 1997
Title: Analysis of the stabilization of hen lysozyme by helix macrodipole and charged side chain interaction.
Authors: Motoshima, H. / Mine, S. / Masumoto, K. / Abe, Y. / Iwashita, H. / Hashimoto, Y. / Chijiiwa, Y. / Ueda, T. / Imoto, T.
History
DepositionNov 22, 1996Processing site: BNL
Revision 1.0Nov 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3321
Polymers14,3321
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.160, 79.160, 37.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein LYSOZYME


Mass: 14332.146 Da / Num. of mol.: 1 / Mutation: N27D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: HEN LYSOZYME / Gene (production host): HEN LYSOZYME / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SACCHAROMYCES CEREVISIAE / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growpH: 4.7 / Details: 50 MM ACETATE AT PH 4.7 CONTAINING 0.9 M NACL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium acetate1reservoirpH4.7
20.9-1.2 M1reservoirNaCl
39.3*10-7 Mprotein1drop
40.1 Msodium acetate1dropwith HCl, pH5.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→100 Å / Num. obs: 8613 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.96→2.02 Å / Rmerge(I) obs: 0.183 / % possible all: 88.2
Reflection
*PLUS
Highest resolution: 1.75 Å / Num. obs: 11948 / % possible obs: 93.2 % / Rmerge(I) obs: 0.0369

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESS(SCALE)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESS(SCALE)data scaling
X-PLOR3.1phasing
RefinementStarting model: PDB ENTRY 1RFP

1rfp


Resolution: 1.96→6 Å / Data cutoff low absF: 1 / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.168 --
obs0.168 8238 93 %
Refinement stepCycle: LAST / Resolution: 1.96→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 62 1063
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.75 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.448

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