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- PDB-7cjz: Room temperature structure of lysozyme delivered in lard by seria... -

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Basic information

Entry
Database: PDB / ID: 7cjz
TitleRoom temperature structure of lysozyme delivered in lard by serial millisecond crystallography
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / serial crystallography / serial millisecond crystallography / serial synchrotron crystallography / lard / delivery medium
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: 1.75 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Lard Injection Matrix for Serial Crystallography.
Authors: Nam, K.H.
History
DepositionJul 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Nov 29, 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)16,3755
Polymers16,2581
Non-polymers1174
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.450, 79.450, 38.470
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-331-

HOH

21A-335-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 16257.660 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.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.87 Å3/Da / Density % sol: 34.12 %
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: 298.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→80 Å / Num. obs: 12954 / % possible obs: 100 % / Redundancy: 385.2 % / CC1/2: 0.9933 / CC star: 0.9983 / Net I/σ(I): 9.84
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 266.8 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1256 / CC1/2: 0.805 / CC star: 0.9444 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IG6

6ig6


Resolution: 1.75→56.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 790 6.12 %
Rwork0.1649 12118 -
obs0.1662 12908 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.73 Å2 / Biso mean: 39.3816 Å2 / Biso min: 21.43 Å2
Refinement stepCycle: final / Resolution: 1.75→56.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 4 58 1063
Biso mean--42.42 41.77 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.860.24461290.197719552084
1.86-20.1881270.163319882115
2-2.20.18171300.156219882118
2.21-2.520.19821300.15720042134
2.52-3.180.20621330.181320332166
3.18-56.180.1711410.159421502291

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