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- PDB-1xft: Synchrotron X-ray Powder Diffraction Study of Hexagonal Turkey Eg... -

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Basic information

Entry
Database: PDB / ID: 1xft
TitleSynchrotron X-ray Powder Diffraction Study of Hexagonal Turkey Egg-white Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / powder diffraction / lysozyme / x-rays
Function / homology
Function and homology information


glycosaminoglycan binding / 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 / 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 speciesMeleagris gallopavo (turkey)
MethodPOWDER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsMargiolaki, I. / Wright, J.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme.
Authors: Margiolaki, I. / Wright, J.P. / Fitch, A.N. / Fox, G.C. / Von Dreele, R.B.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of hexagonal turkey egg-white lysozyme at 1.65A resolution
Authors: Howell, P.L.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution
Authors: Harata, K.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure determination of turkey egg-white lysozyme using Laue diffraction data
Authors: Howell, P.L. / Almo, S.C. / Parsons, M.R. / Hajdu, J. / Petsko, G.A.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Oct 25, 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

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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)14,2281
Polymers14,2281
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 C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14228.105 Da / Num. of mol.: 1 / Fragment: LYSOZYME / Source method: isolated from a natural source / Details: sigma-aldrich chemical company LOT. 064H7230 / Source: (natural) Meleagris gallopavo (turkey) / Tissue: egg white / References: UniProt: P00703, lysozyme

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 295 K / Method: salting out / pH: 6 / Details: NaCl, pH 6, SALTING OUT, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID31 / Wavelength: 0.700667 Å
DetectorType: CUSTOM-MADE / Detector: DIFFRACTOMETER / Date: Dec 3, 2003
Details: DOUBLE SI(111) MONOCHROMATOR, 9 CHANNEL SI(111) MULTI-ANALYSER
RadiationMonochromator: DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.700667 Å / Relative weight: 1
ReflectionResolution: 3.35→95.1 Å / Num. all: 2099 / Num. obs: 2099 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
GSASrefinement
SPECdata reduction
ID31SUMdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TEW

1tew


Resolution: 3.35→95.1 Å / Isotropic thermal model: OVERALL / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: POWDER DIFFRACTION
RfactorNum. reflection% reflectionSelection details
Rwork0.113 ---
obs0.113 2099 100 %-
all-2099 --
Rfree---NOT CURRENTLY APPLICABLE FOR POWDER DATA
Displacement parametersBiso mean: 23.69 Å2
Refinement stepCycle: LAST / Resolution: 3.35→95.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 0 985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.148
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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