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- PDB-3atn: Glycine ethyl ester shielding on the aromatic surfaces of lysozym... -

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Basic information

Entry
Database: PDB / ID: 3atn
TitleGlycine ethyl ester shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation
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: 1.17 Å
AuthorsIto, L. / Shiraki, K. / Hasegawa, K. / Kumasaka, T.
CitationJournal: To be Published
Title: Glycine ethyl ester shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation
Authors: Ito, L. / Shiraki, K. / Hasegawa, K. / Kumasaka, T.
History
DepositionJan 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release

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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)14,70912
Polymers14,3311
Non-polymers37811
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.744, 76.744, 37.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-209-

CL

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hen egg / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.42 %
Crystal growTemperature: 293 K / Method: batch / pH: 4.5
Details: 0.05M sodium acetate, 0.8M sodium chloride, pH 4.5, Batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 8, 2010 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→40 Å / Num. obs: 35863 / % possible obs: 100 %
Reflection shellResolution: 1.17→1.21 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→33.39 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.068 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17377 1883 5 %RANDOM
Rwork0.15122 ---
obs0.15234 35863 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.17→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 11 161 1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211099
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9021499
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37222.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1451513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.2569
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2785
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8731.5682
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.76621094
X-RAY DIFFRACTIONr_scbond_it3.5073444
X-RAY DIFFRACTIONr_scangle_it4.774.5405
X-RAY DIFFRACTIONr_rigid_bond_restr1.98931126
X-RAY DIFFRACTIONr_sphericity_free9.9393173
X-RAY DIFFRACTIONr_sphericity_bonded5.9831068
LS refinement shellResolution: 1.17→1.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 137 -
Rwork0.173 2594 -
obs--98.77 %

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