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- PDB-5k2k: Crystal structure of lysozyme -

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Basic information

Entry
Database: PDB / ID: 5k2k
TitleCrystal structure of lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsKo, S. / Choe, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of lysozyme
Authors: Ko, S. / Choe, J.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 1.2Oct 30, 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
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.361, 77.361, 37.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 IV


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.96 Å3/Da / Density % sol: 37.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris:HCl pH8.5, 1.4M Ammonium Tartrate Dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 14184 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.03 / Rrim(I) all: 0.1 / Χ2: 1.913 / Net I/av σ(I): 45.878 / Net I/σ(I): 8.6 / Num. measured all: 163851
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.545 / Num. unique all: 813 / CC1/2: 0.997 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Χ2: 3.935 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193l

193l


Resolution: 1.65→19.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.001 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 675 4.8 %RANDOM
Rwork0.178 ---
obs0.181 13431 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.16 Å2 / Biso mean: 25.88 Å2 / Biso min: 15.99 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.65→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 117 1118
Biso mean---37.38 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191025
X-RAY DIFFRACTIONr_bond_other_d0.0020.02940
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9031389
X-RAY DIFFRACTIONr_angle_other_deg1.13632140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8872350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72915166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4381511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02271
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_it1.8712.221514
X-RAY DIFFRACTIONr_mcbond_other1.8412.22514
X-RAY DIFFRACTIONr_mcangle_it2.6753.335642
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONSIDE-CHAIN BOND OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B REFINED ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 46 -
Rwork0.202 942 -
all-988 -
obs--100 %

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