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- PDB-4wmg: Structure of hen egg-white lysozyme from a microfludic harvesting... -

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Basic information

Entry
Database: PDB / ID: 4wmg
TitleStructure of hen egg-white lysozyme from a microfludic harvesting device using synchrotron radiation (2.5A)
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / microfluidics / microcrystal / XFEL
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 / Resolution: 2.5 Å
AuthorsLyubimov, A.Y. / Murray, T.D. / Koehl, A. / Uervirojnangkoorn, M. / Zeldin, O.B. / Cohen, A.E. / Soltis, S.M. / Baxter, E.M. / Brewster, A.S. / Sauter, N.K. ...Lyubimov, A.Y. / Murray, T.D. / Koehl, A. / Uervirojnangkoorn, M. / Zeldin, O.B. / Cohen, A.E. / Soltis, S.M. / Baxter, E.M. / Brewster, A.S. / Sauter, N.K. / Brunger, A.T. / Berger, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array.
Authors: Lyubimov, A.Y. / Murray, T.D. / Koehl, A. / Araci, I.E. / Uervirojnangkoorn, M. / Zeldin, O.B. / Cohen, A.E. / Soltis, S.M. / Baxter, E.L. / Brewster, A.S. / Sauter, N.K. / Brunger, A.T. / Berger, J.M.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.250, 79.250, 37.970
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 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.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 3.5
Details: 15% sodium chloride, 6% poly-ethylene glycol 8000 and 0.5M sodium acetate

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2014 / Details: 10 x 10 micron beam
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→22.6 Å / Num. obs: 4696 / % possible obs: 81.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.77 Å2 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.67 % / % possible all: 55.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: DEV_1760) / Classification: refinement
RefinementResolution: 2.5→22.55 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.63 / Phase error: 34.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.306 190 4.91 %RANDOM
Rwork0.274 ---
obs0.275 3870 86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→22.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 3 1004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051045
X-RAY DIFFRACTIONf_angle_d0.9781412
X-RAY DIFFRACTIONf_dihedral_angle_d18.602374
X-RAY DIFFRACTIONf_chiral_restr0.038146
X-RAY DIFFRACTIONf_plane_restr0.003184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.54310.568490.3639151X-RAY DIFFRACTION74
2.5431-2.58930.36280.4038150X-RAY DIFFRACTION72
2.5893-2.6390.290290.3753154X-RAY DIFFRACTION74
2.639-2.69280.528580.3904160X-RAY DIFFRACTION79
2.6928-2.75130.368580.3804176X-RAY DIFFRACTION81
2.7513-2.81520.201360.362168X-RAY DIFFRACTION81
2.8152-2.88540.304680.3462173X-RAY DIFFRACTION84
2.8854-2.96330.407100.332172X-RAY DIFFRACTION82
2.9633-3.05030.290770.3202175X-RAY DIFFRACTION83
3.0503-3.14850.3988100.3287186X-RAY DIFFRACTION89
3.1485-3.26070.262770.2917182X-RAY DIFFRACTION88
3.2607-3.39080.3866110.3042198X-RAY DIFFRACTION92
3.3908-3.54460.2566100.2635186X-RAY DIFFRACTION89
3.5446-3.73070.27110.2273178X-RAY DIFFRACTION86
3.7307-3.96320.2798110.2295197X-RAY DIFFRACTION90
3.9632-4.26730.285490.2293201X-RAY DIFFRACTION95
4.2673-4.69330.3209130.2044212X-RAY DIFFRACTION95
4.6933-5.36440.3068100.2297210X-RAY DIFFRACTION95
5.3644-6.72860.239110.2511215X-RAY DIFFRACTION94
6.7286-22.54620.242140.2427236X-RAY DIFFRACTION95

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