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- PDB-6p4d: Hen egg lysozyme (HEL) containing three point mutations (HEL3x): ... -

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Basic information

Entry
Database: PDB / ID: 6p4d
TitleHen egg lysozyme (HEL) containing three point mutations (HEL3x): R21Q, R73E, and D101R
ComponentsLysozyme C
KeywordsHYDROLASE / hen egg lysozyme HEL3x
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 / molecular replacement / Resolution: 1.05 Å
AuthorsLangley, D.B. / Christ, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens.
Authors: Burnett, D.L. / Schofield, P. / Langley, D.B. / Jackson, J. / Bourne, K. / Wilson, E. / Porebski, B.T. / Buckle, A.M. / Brink, R. / Goodnow, C.C. / Christ, D.
History
DepositionMay 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5737
Polymers14,3161
Non-polymers2576
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-51 kcal/mol
Surface area6400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.550, 77.550, 37.770
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: 14316.123 Da / Num. of mol.: 1 / Mutation: R21Q, R73E, D101R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Cell line (production host): HEK Expi293 / Production host: Homo sapiens (human) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.98 Å3/Da / Density % sol: 37.98 % / Description: large chunks
Crystal growTemperature: 293 K / Method: evaporation
Details: 12 mg/mL protein, 25 mM Tris, pH 8.0, 150 mM sodium chloride, spontaneous crystal growth

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.05→38.77 Å / Num. obs: 54091 / % possible obs: 100 % / Redundancy: 23.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.018 / Rrim(I) all: 0.086 / Net I/σ(I): 20.6 / Num. measured all: 1294996 / Scaling rejects: 3090
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.05-1.0723.70.6236176726100.9470.1320.6374.5100
5.76-38.7719.20.09979254120.9950.0230.10245.199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.68 Å38.77 Å
Translation4.68 Å38.77 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LKS

1lks


Resolution: 1.05→38.77 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.71 / SU ML: 0.016 / SU R Cruickshank DPI: 0.0243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.145 2688 5 %RANDOM
Rwork0.1217 ---
obs0.1227 51340 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 47.7 Å2 / Biso mean: 13.187 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 1.05→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 17 169 1186
Biso mean--19.37 27.04 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181070
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.6371675
X-RAY DIFFRACTIONr_angle_other_deg1.6511.5882482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1895161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10620.78976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00215198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8251514
X-RAY DIFFRACTIONr_chiral_restr0.10.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02298
X-RAY DIFFRACTIONr_rigid_bond_restr1.56932292
LS refinement shellResolution: 1.051→1.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 180 -
Rwork0.216 3731 -
all-3911 -
obs--100 %

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