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- PDB-8cw1: 20us Temperature-Jump (Dark1) XFEL structure of Lysozyme -

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Basic information

Entry
Database: PDB / ID: 8cw1
Title20us Temperature-Jump (Dark1) XFEL structure of Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / temperature-jump / dark1 / 20us / 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
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-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsWolff, A.M. / Thompson, M.C. / Fraser, J.S. / Nango, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
Citation
Journal: Nat.Chem. / Year: 2023
Title: Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.
Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, ...Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, D. / O'Riordan, L.J. / Tanaka, T. / Tanaka, R. / Sierra, R.G. / Yumoto, F. / Tono, K. / Iwata, S. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C.
#1: Journal: Biorxiv / Year: 2022
Title: Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography
Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, ...Authors: Wolff, A.M. / Nango, E. / Young, I.D. / Brewster, A.S. / Kubo, M. / Nomura, T. / Sugahara, M. / Owada, S. / Barad, B.A. / Ito, K. / Bhowmick, A. / Carbajo, S. / Hino, T. / Holton, J.M. / Im, D. / O'Riordan, L.J. / Tanaka, T. / Tanaka, R. / Sierra, R.G. / Yumoto, F. / Tono, K. / Iwata, S. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C.
History
DepositionMay 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_related_exp_data_set
Item: _citation.journal_id_ISSN
Revision 1.2Oct 4, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,6509
Polymers14,3311
Non-polymers3188
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.443, 79.443, 38.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

21A-366-

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 / Fragment: lyzozyme / Source method: obtained synthetically / Source: (synth.) 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 3
Details: Lysozyme [20 mg/ml dissolved in 0.1 M sodium acetate at pH 3.0] mixed with precipitant [28% (w/v) NaCl, 8% (w/v) PEG6000 and 0.1 M sodium acetate at pH 3.0] in a 1:1 ratio

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.57→28.09 Å / Num. obs: 2144941 / % possible obs: 99.97 % / Redundancy: 121.86 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.99 / Net I/σ(I): 10
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 54395 / CC1/2: 0.319
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
cctbx.xfeldata reduction
cxi.mergedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iee

1iee


Resolution: 1.57→28.09 Å / SU ML: 0.1336 / Cross valid method: FREE R-VALUE / σ(F): 1.72 / Phase error: 14.7537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1681 896 5.08 %
Rwork0.1478 16730 -
obs0.1489 17626 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.57→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 94 1109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461135
X-RAY DIFFRACTIONf_angle_d0.76591546
X-RAY DIFFRACTIONf_chiral_restr0.0435158
X-RAY DIFFRACTIONf_plane_restr0.0072210
X-RAY DIFFRACTIONf_dihedral_angle_d13.2137423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.670.25551400.21182740X-RAY DIFFRACTION100
1.67-1.80.20971390.172742X-RAY DIFFRACTION100
1.8-1.980.1681610.13552727X-RAY DIFFRACTION100
1.98-2.260.14791590.12412762X-RAY DIFFRACTION100
2.26-2.850.1751450.1322800X-RAY DIFFRACTION100
2.85-28.090.15161520.15392959X-RAY DIFFRACTION100

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