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- PDB-2aub: Lysozyme structure derived from thin-film-based crystals -

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Basic information

Entry
Database: PDB / ID: 2aub
TitleLysozyme structure derived from thin-film-based crystals
ComponentsLysozyme C
KeywordsHYDROLASE
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPechkova, E. / Sivozhelezov, V. / Tropiano, G. / Fiordoro, S. / Nicolini, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Comparison of lysozyme structures derived from thin-film-based and classical crystals.
Authors: Pechkova, E. / Sivozhelezov, V. / Tropiano, G. / Fiordoro, S. / Nicolini, C.
History
DepositionAug 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.210, 79.210, 37.420
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 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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.93 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755 Å
DetectorDate: May 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.7→27.2 Å / Num. obs: 13598

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
Quantamodel building
XTALVIEWrefinement
REFMAC5refinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27 Å / σ(F): 2.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.283 6799 RANDOM
Rwork0.208 --
all0.22 13598 -
obs0.208 12866 -
Refinement stepCycle: LAST / Resolution: 1.7→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 56 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0241025
X-RAY DIFFRACTIONr_bond_other_d0.0020.021930
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9111389
X-RAY DIFFRACTIONr_angle_other_deg1.01132096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4752350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76115166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.761511
X-RAY DIFFRACTIONr_chiral_restr0.160.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_nbd_refined0.2240.2506
X-RAY DIFFRACTIONr_nbd_other0.1220.2570
X-RAY DIFFRACTIONr_nbtor_refined0.2050.2713
X-RAY DIFFRACTIONr_nbtor_other0.0790.2418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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