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- PDB-2war: Hen Egg White Lysozyme E35Q chitopentaose complex -

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Entry
Database: PDB / ID: 2war
TitleHen Egg White Lysozyme E35Q chitopentaose complex
ComponentsLYSOZYME C
KeywordsHYDROLASE / ANTIMICROBIAL / BACTERIOLYTIC ENZYME / ALLERGEN / GLYCOSIDASE
Function / homologyLysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Alpha-lactalbumin / lysozyme C signature. / Neutrophil degranulation / Alpha-lactalbumin / lysozyme C family profile. / Antimicrobial peptides ...Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Alpha-lactalbumin / lysozyme C signature. / Neutrophil degranulation / Alpha-lactalbumin / lysozyme C family profile. / Antimicrobial peptides / catabolism by organism of cell wall peptidoglycan in other organism / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / killing of cells of other organism / lysozyme / lysozyme activity / cytolysis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm / Lysozyme C
Function and homology information
Specimen sourceGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsDavies, G.J. / Withers, S.G. / Vocadlo, D.J.
CitationJournal: Aust.J.Chem. / Year: 2009
Title: The Chitopentaose Complex of a Mutant Hen Egg-White Lysozyme Displays No Distortion of the -1 Sugar Away from a 4C1 Chair Conformation
Authors: Davies, G.J. / Withers, S.G. / Vocadlo, D.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 13, 2009 / Release: Feb 9, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 9, 2010Structure modelrepositoryInitial release
1.1Jan 11, 2012Structure modelDerived calculations / Non-polymer description / Version format compliance
1.2Feb 5, 2014Structure modelDatabase references / Other
1.3Jan 16, 2019Structure modelData collection / Database referencescitation_citation.pdbx_database_id_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4366
Polyers14,3301
Non-polymers1,1065
Water1,982110
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.632, 78.632, 36.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

#1: Protein/peptide LYSOZYME C / 1\ / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV


Mass: 14330.176 Da / Num. of mol.: 1 / Details: COMPLEX WITH CHITOPENTAOSE / Mutation: YES / Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: EGG WHITE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 5 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Formula: H2O / Water
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 53 TO GLN
Sequence detailsSITE DIRECTED VARIANT E35Q

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.7 / Density percent sol: 27.3 %
Description: THE STRUCTURE OF AN APO E35Q LYSOZYME,UNPUBLISHED, WAS USED AS THE STARTING MODEL. THE CLOSEST PUBLISHED, COORDINATES TO THESE ARE 1H6M, ABOVE
Crystal growpH: 4.5
Details: PROTEIN AT 7MG ML-1 IN 10MM CHITOPENTAOSE 200MM NA ACETATE PH5 WAS MIXED WITH RESERVOIR OF 200MM NA ACETATE, 4% W/V NACL PH4.5

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Details: MIRRORS / Detector: IMAGE PLATE
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 15 Å / Number obs: 11116 / Observed criterion sigma I: -5 / Rmerge I obs: 0.05 / NetI over sigmaI: 4 / Redundancy: 7 % / Percent possible obs: 93
Reflection shellRmerge I obs: 0.28 / Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 6.4 / Redundancy: 6.3 % / Percent possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6M
Correlation coeff Fo to Fc: 0.963 / Correlation coeff Fo to Fc free: 0.941 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. / Overall SU B: 2.312 / Overall SU ML: 0.074 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.145 / Overall ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 14.71 Å2 / Aniso B11: -0.09 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -0.09 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.18 Å2
Least-squares processR factor R free: 0.196 / R factor R work: 0.155 / R factor obs: 0.157 / Highest resolution: 1.8 Å / Lowest resolution: 14.76 Å / Number reflection R free: 507 / Number reflection obs: 9628 / Percent reflection R free: 5 / Percent reflection obs: 91.2
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 14.76 Å
Number of atoms included #LASTProtein: 1001 / Nucleic acid: 0 / Ligand: 71 / Solvent: 110 / Total: 1182
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211107
X-RAY DIFFRACTIONr_bond_other_d0.0010.020749
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9831507
X-RAY DIFFRACTIONr_angle_other_deg1.4953.0001785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895.000129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10423.00050
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71115.000170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.96115.00011
X-RAY DIFFRACTIONr_chiral_restr0.1200.200170
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0201201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.020234
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4151.500638
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2462.0001013
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6783.000469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6094.500493
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.312 / R factor R work: 0.245 / Lowest resolution: 1.85 Å / Number reflection R free: 23 / Number reflection R work: 512 / Total number of bins used: 20

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