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- PDB-2epe: Crystal structure analysis of Hen egg white lysozyme grown by cap... -

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Basic information

Entry
Database: PDB / ID: 2epe
TitleCrystal structure analysis of Hen egg white lysozyme grown by capillary method
ComponentsLysozyme C
KeywordsHYDROLASE / hen egg white 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNaresh, M.D. / Subramanian, V. / Jaimohan, S.M. / Rajaram, A. / Arumugam, V. / Usha, R. / Mandal, A.B.
CitationJournal: To be published
Title: Crystal structure analysis of Hen egg white lysozyme grown by capillary method
Authors: Naresh, M.D. / Subramanian, V. / Jaimohan, S.M. / Rajaram, A. / Arumugam, V. / Usha, R. / Mandal, A.B.
History
DepositionMar 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: 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: Refinement description / Category: software / Item: _software.name
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)14,3311
Polymers14,3311
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.243, 79.243, 37.829
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) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 298 K / Method: capillary method / pH: 4.7
Details: 0.04m NAOAC/HOAC buffer, pH 4.7, capillary method, temperature 298.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→39.53 Å / Num. obs: 4332 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 22.02 Å2
Reflection shellResolution: 2.5→39.53 Å / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 5.9 / Num. unique all: 4332 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345345DTBdata collection
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 193L

193l


Resolution: 2.5→39.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.908 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21131 203 4.6 %RANDOM
Rwork0.16454 ---
obs0.16681 4189 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 48 1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0211025
X-RAY DIFFRACTIONr_bond_other_d0.0070.02883
X-RAY DIFFRACTIONr_angle_refined_deg2.4411.9061388
X-RAY DIFFRACTIONr_angle_other_deg1.96432043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4593128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00715172
X-RAY DIFFRACTIONr_chiral_restr0.1750.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021172
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02229
X-RAY DIFFRACTIONr_nbd_refined0.240.3229
X-RAY DIFFRACTIONr_nbd_other0.220.3871
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.546
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2480.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4270.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3840.39
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.3040.53
X-RAY DIFFRACTIONr_symmetry_hbond_other0.5750.51
X-RAY DIFFRACTIONr_mcbond_it1.9391.5635
X-RAY DIFFRACTIONr_mcangle_it3.23521007
X-RAY DIFFRACTIONr_scbond_it4.9073390
X-RAY DIFFRACTIONr_scangle_it7.4354.5381
LS refinement shellResolution: 2.504→2.569 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 19
Rwork0.161 295

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