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- PDB-2hs9: Multipattern Rietveld refinement with protein powder data: An app... -

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Basic information

Entry
Database: PDB / ID: 2hs9
TitleMultipattern Rietveld refinement with protein powder data: An approach to higher resolution
ComponentsLysozyme C
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: 1.98 Å
AuthorsVon Dreele, R.B.
CitationJournal: J.APPL.CRYSTALLOGR. / Year: 2007
Title: Multipattern Rietveld refinement with protein powder data: an approach to higher resolution
Authors: Von Dreele, R.B.
History
DepositionJul 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsASYMMETRIC UNIT CONTAINS ONE MOLECULE WHICH IS BIOLOGICAL ASSEMBLY

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Components

#1: Protein Lysozyme C / 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) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 298 K / Method: batch crystallization / pH: 5
Details: Rapid precipitation for 4 samples from 1.25, 1.0, 0.75 AND 0.25M NaCl in 0.05M KHPHTHALATE BUFFER, pH 5.0, BATCH CRYSTALLIZATION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 1-BM-C / Wavelength: 0.62074 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 2004
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthWavelength: 0.62074 Å / Relative weight: 1
ReflectionResolution: 1.98→17.77 Å / Num. all: 8825 / Num. obs: 8776 / % possible obs: 99.9 % / Redundancy: 3.986 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.02

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Processing

Software
NameClassification
GSASrefinement
FIT2Ddata reduction

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