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- PDB-7ynv: Crystal structure of photolysed Hen Egg white LYSOZYME introduced... -

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Basic information

Entry
Database: PDB / ID: 7ynv
TitleCrystal structure of photolysed Hen Egg white LYSOZYME introduced with O-(2-nitrobenzyl)-L-tyrosine
ComponentsLysozyme C
KeywordsBIOSYNTHETIC PROTEIN / nonnatural amino acid caged amino acid o-(2-nitrobenzyl)-L-tyrosine lysozyme cell-free protein synthesis
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsHosaka, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Int J Mol Sci / Year: 2022
Title: Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography.
Authors: Hosaka, T. / Katsura, K. / Ishizuka-Katsura, Y. / Hanada, K. / Ito, K. / Tomabechi, Y. / Inoue, M. / Akasaka, R. / Takemoto, C. / Shirouzu, M.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)14,6198
Polymers14,3591
Non-polymers2597
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-24 kcal/mol
Surface area6470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.280, 78.280, 37.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 14359.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.6 / Details: 28% NaCl, 8% PEG6000, 100 mM Na-acetate (pH3.6)

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→39.14 Å / Num. obs: 23873 / % possible obs: 99.5 % / Redundancy: 22.06 % / Biso Wilson estimate: 16.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.124 / Χ2: 0.726 / Net I/σ(I): 23.06 / Num. measured all: 526644 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.39-1.4717.8390.3737.0162580362435080.970.38496.8
1.47-1.5823.4480.24712.7990816387338730.9930.253100
1.58-1.723.3060.18318.0374089317931790.9970.187100
1.7-1.8622.5230.15722.3968987306330630.9970.161100
1.86-2.0821.9640.13828.3862421284228420.9980.142100
2.08-2.4123.7780.12734.7461109257025700.9850.13100
2.41-2.9522.9750.11836.8348685211921190.9980.121100
2.95-4.1720.8080.11337.0735581171017100.9970.116100
4.17-39.1422.1760.10938.822376101210090.9970.11199.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YM8

4ym8


Resolution: 1.39→39.14 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 2000 8.39 %
Rwork0.1742 21825 -
obs0.1757 23825 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.96 Å2 / Biso mean: 21.1301 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 1.39→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 10 138 1150
Biso mean--26.19 32.83 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.39-1.420.25381310.23061441157293
1.42-1.460.20891400.216115171657100
1.46-1.510.26241420.191615481690100
1.51-1.550.23021400.184115371677100
1.56-1.610.21911410.187215311672100
1.61-1.680.1991420.182115471689100
1.68-1.750.22181420.211415431685100
1.75-1.840.21351420.184615541696100
1.84-1.960.22721420.17715631705100
1.96-2.110.20021450.168915611706100
2.11-2.320.1951430.163715731716100
2.32-2.660.1871460.170415861732100
2.66-3.350.1891480.169916151763100
3.35-39.140.16021560.164917091865100

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