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- PDB-6ig6: Crystal structure of lysozyme delivered in polyacrylamide using x... -

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Basic information

Entry
Database: PDB / ID: 6ig6
TitleCrystal structure of lysozyme delivered in polyacrylamide using x-ray free electron laser
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / xfel / serial femtosecond crystallography / sfx / x-ray free electron laser
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 / molecular replacement / Resolution: 1.7 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2019
Title: Polyacrylamide injection matrix for serial femtosecond crystallography.
Authors: Park, J. / Park, S. / Kim, J. / Park, G. / Cho, Y. / Nam, K.H.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 1.4Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_R_split
Revision 1.5Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.7Oct 16, 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)14,4254
Polymers14,3311
Non-polymers943
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.600, 79.600, 38.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-339-

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: 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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293.5 K / Method: small tubes / Details: sodium acetate, PEG 8000, NaCl

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 15, 2018 / Frequency: 30 / Details: KB mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.7→80 Å / Num. obs: 14007 / % possible obs: 100 % / Redundancy: 965.3 % / Biso Wilson estimate: 38.88 Å2 / CC1/2: 0.99 / R split: 0.1531 / Net I/σ(I): 4.32
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 676.7 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 1353 / CC1/2: 0.64 / R split: 0.7337 / % possible all: 100
Serial crystallography measurementCollection time total: 0.3 hours / Collimation: Kirkpatrick-Baez mirrors / Focal spot size: 5 µm2 / Pulse duration: 20 fsec. / Pulse photon energy: 9.7 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Injector / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: polyacrylamide / Crystal conc.: 67000000 / Description: CMD (Carrier matrix delivery) injector / Flow rate: 800 µL/min / Injector diameter: 100 µm / Injector nozzle: gas / Jet diameter: 100 µm / Power by: HPLC / Preparation: crystals delivered in polyacrylamide
Serial crystallography data reductionCrystal hits: 17675 / Frame hits: 17675 / Frames failed index: 5739 / Frames indexed: 11936 / Frames total: 25603 / Lattices indexed: 11936

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ET8

4et8


Resolution: 1.7→26.043 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.57
RfactorNum. reflection% reflection
Rfree0.2174 953 6.8 %
Rwork0.1961 --
obs0.1976 14005 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.71 Å2 / Biso mean: 45.0368 Å2 / Biso min: 26.4 Å2
Refinement stepCycle: final / Resolution: 1.7→26.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 39 1043
Biso mean--45.81 46.2 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081054
X-RAY DIFFRACTIONf_angle_d0.9411432
X-RAY DIFFRACTIONf_chiral_restr0.054146
X-RAY DIFFRACTIONf_plane_restr0.006187
X-RAY DIFFRACTIONf_dihedral_angle_d14.545626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.78970.3151310.27718021933
1.7897-1.90180.35781340.286618361970
1.9018-2.04850.19771340.187718361970
2.0485-2.25460.21181350.177518471982
2.2546-2.58060.19621350.173518561991
2.5806-3.25030.20621380.195218802018
3.2503-26.0460.22091460.199319952141

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