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- PDB-6h0l: Hen egg-white lysozyme structure determined with data from the Eu... -

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Basic information

Entry
Database: PDB / ID: 6h0l
TitleHen egg-white lysozyme structure determined with data from the EuXFEL, 9.22 keV photon energy
ComponentsLysozyme C
KeywordsHYDROLASE / Free-electron laser / serial crystallography / lectin
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGruenbein, M.L. / Gorel, A. / Stricker, M. / Bean, R. / Bielecki, J. / Doerner, K. / Hartmann, E. / Hilpert, M. / Kloos, M. / Letrun, R. ...Gruenbein, M.L. / Gorel, A. / Stricker, M. / Bean, R. / Bielecki, J. / Doerner, K. / Hartmann, E. / Hilpert, M. / Kloos, M. / Letrun, R. / Sztuk-Dambietz, J. / Mancuso, A. / Meserschmidt, M. / Nass-Kovacs, G. / Ramilli, M. / Roome, C.M. / Sato, T. / Doak, R.B. / Shoeman, R.L. / Foucar, L. / Colletier, J.P. / Barends, T.R.M. / Stan, C. / Schlichting, I.
CitationJournal: Nat Commun / Year: 2018
Title: Megahertz data collection from protein microcrystals at an X-ray free-electron laser.
Authors: Grunbein, M.L. / Bielecki, J. / Gorel, A. / Stricker, M. / Bean, R. / Cammarata, M. / Dorner, K. / Frohlich, L. / Hartmann, E. / Hauf, S. / Hilpert, M. / Kim, Y. / Kloos, M. / Letrun, R. / ...Authors: Grunbein, M.L. / Bielecki, J. / Gorel, A. / Stricker, M. / Bean, R. / Cammarata, M. / Dorner, K. / Frohlich, L. / Hartmann, E. / Hauf, S. / Hilpert, M. / Kim, Y. / Kloos, M. / Letrun, R. / Messerschmidt, M. / Mills, G. / Nass Kovacs, G. / Ramilli, M. / Roome, C.M. / Sato, T. / Scholz, M. / Sliwa, M. / Sztuk-Dambietz, J. / Weik, M. / Weinhausen, B. / Al-Qudami, N. / Boukhelef, D. / Brockhauser, S. / Ehsan, W. / Emons, M. / Esenov, S. / Fangohr, H. / Kaukher, A. / Kluyver, T. / Lederer, M. / Maia, L. / Manetti, M. / Michelat, T. / Munnich, A. / Pallas, F. / Palmer, G. / Previtali, G. / Raab, N. / Silenzi, A. / Szuba, J. / Venkatesan, S. / Wrona, K. / Zhu, J. / Doak, R.B. / Shoeman, R.L. / Foucar, L. / Colletier, J.P. / Mancuso, A.P. / Barends, T.R.M. / Stan, C.A. / Schlichting, I.
History
DepositionJul 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.050, 80.050, 38.600
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 3 / Details: 20% NaCl, 6% PEG 6000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.344 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.344 Å / Relative weight: 1
ReflectionResolution: 1.9→36 Å / Num. obs: 18913 / % possible obs: 100 % / Redundancy: 278 % / R split: 0.154 / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2.9 / R split: 0.591

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GF0

6gf0


Resolution: 1.9→28.302 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.84
RfactorNum. reflection% reflection
Rfree0.2373 1035 10 %
Rwork0.188 --
obs0.1931 10346 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 80 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081016
X-RAY DIFFRACTIONf_angle_d1.0541368
X-RAY DIFFRACTIONf_dihedral_angle_d13.649361
X-RAY DIFFRACTIONf_chiral_restr0.045142
X-RAY DIFFRACTIONf_plane_restr0.004179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.27791440.24411285X-RAY DIFFRACTION100
2.0002-2.12550.28481430.20961309X-RAY DIFFRACTION100
2.1255-2.28950.23771450.18491311X-RAY DIFFRACTION100
2.2895-2.51980.23221480.18241297X-RAY DIFFRACTION100
2.5198-2.88410.24891460.19041325X-RAY DIFFRACTION100
2.8841-3.63240.23771470.17411347X-RAY DIFFRACTION100
3.6324-28.30510.21051620.18131437X-RAY DIFFRACTION100

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