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- PDB-1sfb: BINDING OF PENTA-N-ACETYLCHITOPENTAOSE TO HEW LYSOZYME: A POWDER ... -

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Basic information

Entry
Database: PDB / ID: 1sfb
TitleBINDING OF PENTA-N-ACETYLCHITOPENTAOSE TO HEW 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 / Resolution: 3.22 Å
AuthorsVon Dreele, R.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Binding of N-acetylglucosamine oligosaccharides to hen egg-white 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 High 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.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Binding of N-Acetylglucoasmine to Chicken Egg Lysozyme: A Powder Diffraction Study
Authors: Von Dreele, R.B.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers14,3311
Non-polymers1,0341
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
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: rapid precipitation / pH: 6
Details: NaCl, Na2HPO4, KH2PO4, penta-N-acetylchitopentaose, pH 6.0, rapid precipitation, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 1.0 M / Details: pH6.0 / Chemical formula: NaCl

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3B1 / Wavelength: 0.700388 Å
DetectorType: CUSTOM-MADE / Detector: DIFFRACTOMETER / Date: Jul 21, 2001 / Details: Ge(111) analyser
RadiationMonochromator: double Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.700388 Å / Relative weight: 1
ReflectionResolution: 3.22→40.13 Å / Num. all: 2254 / Num. obs: 2254 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
povdata collection
PROCESSdata reduction
GSASmodel building
GSASrefinement
POVdata reduction
PROCESSdata scaling
GSASphasing

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