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- PDB-5dla: Structure of Tetragonal Lysozyme solved by UWO Students -

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Basic information

Entry
Database: PDB / ID: 5dla
TitleStructure of Tetragonal Lysozyme solved by UWO Students
ComponentsLysozyme C
KeywordsHYDROLASE / Glycoside Hydrolase / Enzyme
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 / Resolution: 1.22 Å
AuthorsBednarski, R. / Cirricione, N. / Greco, A. / Hodgson, R. / Kent, S. / McGowan, J. / Notherm, B. / Patt, M. / Vue, L. / Bianchetti, C.M.
CitationJournal: To Be Published
Title: Structure of Tetragonal Lysozyme in complex with Iodine solved by UWO Students
Authors: Bednarski, R. / Cirricione, N. / Greco, A. / Hodgson, R. / Kent, S. / McGowan, J. / Notherm, B. / Patt, M. / Vue, L. / Bianchetti, C.M.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,76611
Polymers14,3311
Non-polymers43410
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.938, 78.938, 36.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21A-372-

HOH

31A-492-

HOH

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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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Protein Solution (60 mg/ml protein in 0.1M Na acetate pH 4.6) mixed in a 1:1 ratio with the Well Solution (10% NaCl buffered in 0.1 M Na acetate pH 4.5). Cryoprotected in 10% NaCl, 0.1 M Na ...Details: Protein Solution (60 mg/ml protein in 0.1M Na acetate pH 4.6) mixed in a 1:1 ratio with the Well Solution (10% NaCl buffered in 0.1 M Na acetate pH 4.5). Cryoprotected in 10% NaCl, 0.1 M Na acetate pH 4.5 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.22→33.41 Å / Num. obs: 34007 / % possible obs: 96.46 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 43.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DL9

5dl9


Resolution: 1.22→33.41 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1641 1701 5 %
Rwork0.1368 --
obs0.1382 32054 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 19 196 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061086
X-RAY DIFFRACTIONf_angle_d1.0491462
X-RAY DIFFRACTIONf_dihedral_angle_d12.41402
X-RAY DIFFRACTIONf_chiral_restr0.047150
X-RAY DIFFRACTIONf_plane_restr0.004192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.25590.16651100.1262090X-RAY DIFFRACTION77
1.2559-1.29650.13871270.11612413X-RAY DIFFRACTION88
1.2965-1.34280.16271390.11912628X-RAY DIFFRACTION96
1.3428-1.39660.14981430.12052739X-RAY DIFFRACTION100
1.3966-1.46010.16371460.1142765X-RAY DIFFRACTION100
1.4601-1.53710.12051450.1162757X-RAY DIFFRACTION100
1.5371-1.63340.14351460.11692757X-RAY DIFFRACTION100
1.6334-1.75950.15941470.12832795X-RAY DIFFRACTION100
1.7595-1.93660.15351470.13282793X-RAY DIFFRACTION100
1.9366-2.21680.14541460.1352801X-RAY DIFFRACTION100
2.2168-2.79270.1741500.15222850X-RAY DIFFRACTION100
2.7927-33.42720.19371550.15412918X-RAY DIFFRACTION97

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