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- PDB-4et8: Hen egg-white lysozyme solved from 40 fs free-electron laser puls... -

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Basic information

Entry
Database: PDB / ID: 4et8
TitleHen egg-white lysozyme solved from 40 fs free-electron laser pulse data
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme
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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBoutet, S. / Lomb, L. / Williams, G. / Barends, T. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D. / Steinbrener, J. / Shoeman, R. ...Boutet, S. / Lomb, L. / Williams, G. / Barends, T. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D. / Steinbrener, J. / Shoeman, R. / Messerschmidt, M. / Barty, A. / White, T. / Kassemeyer, S. / Kirian, R. / Seibert, M. / Montanez, P. / Kenney, C. / Herbst, R. / Hart, P. / Pines, J. / Haller, G. / Gruner, S. / Philllip, H. / Tate, M. / Hromalik, M. / Koerner, L. / van Bakel, N. / Morse, J. / Ghonsalves, W. / Arnlund, D. / Bogan, M. / Calemann, C. / Fromme, R. / Hampton, C. / Hunter, M. / Johansson, L. / Katona, G. / Kupitz, C. / Liang, M. / Martin, A. / Nass, K. / Redecke, L. / Stellato, F. / Timneanu, N. / Wang, D. / Zatsepin, N. / Schafer, D. / Defever, K. / Neutze, R. / Fromme, P. / Spence, J. / Chapman, H. / Schlichting, I.
CitationJournal: Science / Year: 2012
Title: High-resolution protein structure determination by serial femtosecond crystallography.
Authors: Boutet, S. / Lomb, L. / Williams, G.J. / Barends, T.R. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D.P. / Steinbrener, J. / Shoeman, R.L. / Messerschmidt, M. / Barty, A. / White, T. ...Authors: Boutet, S. / Lomb, L. / Williams, G.J. / Barends, T.R. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D.P. / Steinbrener, J. / Shoeman, R.L. / Messerschmidt, M. / Barty, A. / White, T.A. / Kassemeyer, S. / Kirian, R.A. / Seibert, M.M. / Montanez, P.A. / Kenney, C. / Herbst, R. / Hart, P. / Pines, J. / Haller, G. / Gruner, S.M. / Philipp, H.T. / Tate, M.W. / Hromalik, M. / Koerner, L.J. / van Bakel, N. / Morse, J. / Ghonsalves, W. / Arnlund, D. / Bogan, M.J. / Caleman, C. / Fromme, R. / Hampton, C.Y. / Hunter, M.S. / Johansson, L.C. / Katona, G. / Kupitz, C. / Liang, M. / Martin, A.V. / Nass, K. / Redecke, L. / Stellato, F. / Timneanu, N. / Wang, D. / Zatsepin, N.A. / Schafer, D. / Defever, J. / Neutze, R. / Fromme, P. / Spence, J.C. / Chapman, H.N. / Schlichting, I.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Nov 18, 2015Group: Other
Revision 1.3Nov 15, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,3903
Polymers14,3311
Non-polymers582
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 79.000, 38.000
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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 12247

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 293 K / Method: batch
Details: After crystallization, the solution used for growing the crystals (20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0) was exchanged for storage solution (10 % NaCl, 1.0 M Na acetate pH 3.4), BATCH, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.32 Å
DetectorDetector: PIXEL / Date: Feb 1, 2011 / Details: Be lenses
RadiationMonochromator: CXI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32 Å / Relative weight: 1
ReflectionResolution: 1.9→35.3 Å / Num. all: 9921 / Num. obs: 9921 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
CXIDAQdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→35.3 Å / SU ML: 0.52 / σ(F): 1.53 / σ(I): 0 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 505 5.09 %RANDOM
Rwork0.1961 ---
obs0.1978 9920 99.99 %-
all-9920 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.808 Å2 / ksol: 0.293 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.929 Å2-0 Å20 Å2
2---0.929 Å20 Å2
3---1.858 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 87 1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061025
X-RAY DIFFRACTIONf_angle_d0.9841381
X-RAY DIFFRACTIONf_dihedral_angle_d13.671365
X-RAY DIFFRACTIONf_chiral_restr0.076144
X-RAY DIFFRACTIONf_plane_restr0.003181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.09120.23261280.21672274X-RAY DIFFRACTION100
2.0912-2.39370.22281210.16892321X-RAY DIFFRACTION100
2.3937-3.01560.22371280.18372341X-RAY DIFFRACTION100
3.0156-35.3360.23331280.20532479X-RAY DIFFRACTION100

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