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- PDB-1ja2: BINDING OF N-ACETYLGLUCOSAMINE TO CHICKEN EGG LYSOZYME: A POWDER ... -

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Basic information

Entry
Database: PDB / ID: 1ja2
TitleBINDING OF N-ACETYLGLUCOSAMINE TO CHICKEN EGG LYSOZYME: A POWDER DIFFRACTION STUDY
ComponentsLYSOZYME
KeywordsHYDROLASE / POWDER DIFFRACTION / RIETVELD REFINEMENT / LYSOZYME
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
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-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodPOWDER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsVon Dreele, R.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study.
Authors: Von Dreele, R.B.
#1: Journal: J.Appl.Crystallogr. / Year: 1999
Title: Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure
Authors: Von Dreele, R.B.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The First Protein Crystal Structure Determined from Resolution X-Ray Powder Diffraction Data: A Variant of the T3R3 Human Insulin Zinc Complex Produced by Grinding
Authors: Von Dreele, R.B. / Stephens, P.W. / Blessing, R.H. / Smith, G.D.
History
DepositionMay 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein LYSOZYME / E.C.3.2.1.17 / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D 4 / GAL D IV


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 296 K / Method: precipitation / pH: 4.8
Details: rapid precipitation from 0.5M NACL IN PH 5.0 0.05M KHPHTHALATE/NAOH BUFFER, at 296K, pH 4.8
Crystal grow
*PLUS
Method: unknown / Details: Von Dreele, R.B., (2000) Acta Cryst., D56, 1549.
Components of the solutions
*PLUS
Conc.: 1.0 M / Chemical formula: NaCl

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3B1 / Wavelength: 0.70003 Å
DetectorDetector: SCINTILLATOR / Date: Oct 23, 2000 / Details: 2MM X 8MM BEAM
RadiationMonochromator: DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthWavelength: 0.70003 Å / Relative weight: 1
ReflectionResolution: 2.87→40.03 Å / Num. all: 3112 / Num. obs: 3112 / % possible obs: 100 %

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Processing

Software
NameClassification
PROCESSdata reduction
GSASrefinement
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RFP

1rfp


Resolution: 2.87→40.03 Å / Isotropic thermal model: Overall fixed / Stereochemistry target values: Engh & Huber
Details: Used band matrix least squares, band width 300 parameters
Num. reflection% reflection
all3112 -
obs3112 100 %
Displacement parametersBiso mean: 23.7 Å2
Refinement stepCycle: LAST / Resolution: 2.87→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 0 1001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.71
X-RAY DIFFRACTIONo_bond_d0.027

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