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- PDB-6irj: Crystal structure of lysozyme by fixed-target serial femtosecond ... -

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Basic information

Entry
Database: PDB / ID: 6irj
TitleCrystal structure of lysozyme by fixed-target serial femtosecond crystallography
ComponentsLysozyme C
KeywordsHYDROLASE / SFX / serial femtosecond crystallography
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: 1.65 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017M3A9F6029736 Korea, Republic Of
National Research Foundation (Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2019
Title: Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography.
Authors: Lee, D. / Baek, S. / Park, J. / Lee, K. / Kim, J. / Lee, S.J. / Chung, W.K. / Lee, J.L. / Cho, Y. / Nam, K.H.
History
DepositionNov 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 1.3Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_R_split
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This protein has been characterized the oligomeric state by using the gel filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.220, 78.220, 37.760
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-327-

HOH

21A-342-

HOH

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Components

#1: Protein Lysozyme C


Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147
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.: 42 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 293.5 K / Method: small tubes / pH: 4.5 / Details: sodium acetate, PEG 8000, NaCl

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Data collection

DiffractionMean temperature: 296 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: CSI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 29, 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: 1.65→80 Å / Num. obs: 29127 / % possible obs: 100 % / Redundancy: 4660.8 % / CC1/2: 0.985 / R split: 0.1028 / Net I/σ(I): 6.61
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 962.2 % / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2861 / CC1/2: 0.37 / R split: 0.7873 / % possible all: 100
Serial crystallography measurementCollection time total: 1.2 hours / Collimation: Kirkpatrick-Baez mirrors / Focal spot size: 4 µm2 / Pulse duration: 20 fsec. / Pulse photon energy: 9700 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: seal / Sample holding: mesh / Sample unit size: 30 µm
Serial crystallography data reductionFrame hits: 118985 / Frames total: 133107 / XFEL pulse events: 10000 / XFEL run numbers: 14

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHASERphasing
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IG6

6ig6


Resolution: 1.65→55.31 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.26
RfactorNum. reflection% reflection
Rfree0.2286 2557 9.49 %
Rwork0.2046 --
obs0.2069 26937 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.25 Å2 / Biso mean: 44.4569 Å2 / Biso min: 27.3 Å2
Refinement stepCycle: final / Resolution: 1.65→55.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 42 1046
Biso mean--41.45 45.74 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.68170.3391380.317613401478
1.6817-1.71610.29241460.278413801526
1.7161-1.75340.29541400.265513361476
1.7534-1.79420.45431390.383213501489
1.7942-1.8390.41491450.319713611506
1.839-1.88880.25371470.246513741521
1.8888-1.94440.2381360.16313441480
1.9444-2.00710.17381400.159813571497
2.0071-2.07890.23391410.168313441485
2.0789-2.16210.20221410.161413661507
2.1621-2.26050.20491420.169213451487
2.2605-2.37970.14361440.163913571501
2.3797-2.52880.23191440.175713631507
2.5288-2.7240.19951460.18913471493
2.724-2.99810.23781400.210413481488
2.9981-3.43190.23121450.209413631508
3.4319-4.32360.21141430.217113551498
4.3236-55.3410.26761400.229113501490

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