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- PDB-2yvb: High resolution X-ray crystal structure of Tetragonal Hen egg whi... -

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Basic information

Entry
Database: PDB / ID: 2yvb
TitleHigh resolution X-ray crystal structure of Tetragonal Hen egg white lysozyme
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: 1.62 Å
AuthorsNaresh, M.D. / Jaimohan, S.M. / Kumar, V.V. / Mandal, A.B.
CitationJournal: To be Published
Title: High resolution X-ray crystal structure of Tetragonal Hen egg white lysozyme
Authors: Naresh, M.D. / Jaimohan, S.M. / Kumar, V.V.
History
DepositionApr 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 4, 2013Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 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
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.341, 79.341, 37.867
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) / Cellular location: Egg white / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.7
Details: 0.04N NaOAc/HOAc buffer, pH 4.7, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
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: 1.62→55.9 Å / Num. all: 15495 / Num. obs: 15495 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 23.872 Å2
Reflection shellHighest resolution: 1.62 Å / Num. unique all: 15495 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345345data collection
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 193L

193l


Resolution: 1.62→28.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.28 / SU ML: 0.175 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 789 5 %RANDOM
Rwork0.22855 ---
all0.23095 15495 --
obs0.23095 15495 98.55 %-
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: 23.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.62→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 81 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0211025
X-RAY DIFFRACTIONr_bond_other_d0.0020.02883
X-RAY DIFFRACTIONr_angle_refined_deg2.5931.9061388
X-RAY DIFFRACTIONr_angle_other_deg1.36632043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9893128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6515172
X-RAY DIFFRACTIONr_chiral_restr0.1680.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021172
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02229
X-RAY DIFFRACTIONr_nbd_refined0.2360.3233
X-RAY DIFFRACTIONr_nbd_other0.220.3853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.562
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4530.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4930.311
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5060.56
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2070.52
X-RAY DIFFRACTIONr_mcbond_it1.9511.5635
X-RAY DIFFRACTIONr_mcangle_it2.67721007
X-RAY DIFFRACTIONr_scbond_it3.9993390
X-RAY DIFFRACTIONr_scangle_it5.9724.5381
LS refinement shellResolution: 1.617→1.659 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.461 67
Rwork0.451 1080

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