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- PDB-3ln2: Crystal Structure of a Charge Engineered Human Lysozyme Variant -

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Basic information

Entry
Database: PDB / ID: 3ln2
TitleCrystal Structure of a Charge Engineered Human Lysozyme Variant
ComponentsLysozyme C
KeywordsHYDROLASE / Human Lysozyme / Charge Engineered human lysozyme / Protein engineering / Antimicrobial / Bacteriolytic / Surface Mutation / Amyloid / Amyloidosis / Bacteriolytic enzyme / Disease mutation / Disulfide bond / Glycosidase
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.037 Å
AuthorsGill, A. / Scanlon, T.C. / Griswold, K.E.
CitationJournal: Plos One / Year: 2011
Title: Crystal structure of a charge engineered human lysozyme having enhanced bactericidal activity.
Authors: Gill, A. / Scanlon, T.C. / Osipovitch, D.C. / Madden, D.R. / Griswold, K.E.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)29,3192
Polymers29,3192
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,6601
Polymers14,6601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,6601
Polymers14,6601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.421, 63.795, 111.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14659.539 Da / Num. of mol.: 2 / Mutation: R101D, R115H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ, LZM / Plasmid: pRS416-GAL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5464 / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 20mM Na-Acetate, 1.25M NaCl, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2009 / Details: Xenocs FOX-2D Multilayer Mirrors
RadiationMonochromator: Xenocs FOX-2D Multilayer Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.03→19.86 Å / Num. all: 20170 / Num. obs: 19855 / % possible obs: 98.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 9.49 / Net I/σ(I): 21.58
Reflection shellResolution: 2.03→2.14 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 9.49 / % possible all: 90.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX1.5_2model building
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.5_2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LZS

1lzs


Resolution: 2.037→19.859 Å / SU ML: 0.24 / Cross valid method: ML / σ(F): 2.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1033 5.2 %IN THIN SHELLS
Rwork0.1813 ---
obs0.1835 19848 99.6 %-
all-20170 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.02 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 1.0618 Å2
Baniso -1Baniso -2Baniso -3
1-5.7241 Å2-0 Å2-0 Å2
2---2.9845 Å20 Å2
3----2.7396 Å2
Refinement stepCycle: LAST / Resolution: 2.037→19.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 0 237 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082100
X-RAY DIFFRACTIONf_angle_d1.0142832
X-RAY DIFFRACTIONf_dihedral_angle_d15.322742
X-RAY DIFFRACTIONf_chiral_restr0.076292
X-RAY DIFFRACTIONf_plane_restr0.004374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0375-2.14480.22991340.17692599X-RAY DIFFRACTION98
2.1448-2.2790.21431140.15772687X-RAY DIFFRACTION100
2.279-2.45470.21641950.16892604X-RAY DIFFRACTION100
2.4547-2.70110.2241380.18652673X-RAY DIFFRACTION100
2.7011-3.09070.24521350.19422696X-RAY DIFFRACTION100
3.0907-3.88920.22871420.17552730X-RAY DIFFRACTION100
3.8892-19.860.19411750.17312826X-RAY DIFFRACTION100

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