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- PDB-8h8t: Room-temperature structure of lysozyme by pink-beam serial crysta... -

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Basic information

Entry
Database: PDB / ID: 8h8t
TitleRoom-temperature structure of lysozyme by pink-beam serial crystallography (50 ms, edge)
ComponentsLysozyme C
KeywordsHYDROLASE / pink-beam / serial synchrotron crystallography / room-temperature
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKim, Y. / Nam, K.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
Citation
Journal: Data Brief / Year: 2024
Title: Data of pink-beam serial synchrotron crystallography at the Pohang Light Source II.
Authors: Kim, Y. / Nam, K.H.
#1: Journal: Crystals / Year: 2022
Title: Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II
Authors: Kim, Y. / Nam, K.H.
History
DepositionOct 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Nov 13, 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)14,4254
Polymers14,3311
Non-polymers943
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
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)78.880, 78.880, 38.050
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-332-

HOH

21A-368-

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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.06 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 298.5 K / Method: small tubes / Details: Na-acetate, NaCl, PEG 8000

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Data collection

DiffractionMean temperature: 299.5 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.8009 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2022
RadiationMonochromator: Mo/B4C multilayer, 1.2 % BW / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8009 Å / Relative weight: 1
ReflectionResolution: 1.7→80.6 Å / Num. obs: 14189 / % possible obs: 100 % / Redundancy: 925.4 % / CC1/2: 0.988 / CC star: 0.9969 / Net I/σ(I): 6.78
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 1380 / CC1/2: 0.4404 / CC star: 0.782
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WUC

7wuc


Resolution: 1.7→55.78 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 902 6.6 %
Rwork0.2114 12759 -
obs0.2128 13661 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.02 Å2 / Biso mean: 23.07 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: final / Resolution: 1.7→55.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 88 1092
Biso mean--26.28 35.47 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.810.33211480.281820922240100
1.81-1.950.30491480.249320862234100
1.95-2.140.28161490.213521142263100
2.14-2.450.22791490.185721102259100
2.45-3.090.21131520.187721442296100
3.09-55.780.19971560.21542213236997

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