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- PDB-7ynu: Crystal structure of Hen Egg white LYSOZYME introduced with O-(2-... -

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Basic information

Entry
Database: PDB / ID: 7ynu
TitleCrystal structure of 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: 1.44 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7548
Polymers14,4941
Non-polymers2597
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.680, 79.680, 37.050
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: 14494.332 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.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.71 %
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: 1.44→39.84 Å / Num. obs: 22119 / % possible obs: 99.6 % / Redundancy: 15.849 % / Biso Wilson estimate: 20.55 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.223 / Rrim(I) all: 0.232 / Χ2: 0.658 / Net I/σ(I): 5.62 / Num. measured all: 350557 / Scaling rejects: 279
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
1.44-1.5315.5640.8721.0655953359835950.7410.90199.9
1.53-1.6316.4240.5961.8451637314831440.8280.61599.9
1.63-1.7616.2280.4482.8850015310030820.90.46399.4
1.76-1.9315.4040.3724.3844086289428620.9230.38698.9
1.93-2.1616.020.316.9842181264326330.9460.3299.6
2.16-2.4916.4430.2859.3637737230222950.9430.29699.7
2.49-3.0515.8270.23310.9531512199419910.9580.24299.8
3.05-4.3214.5550.19712.322881157815720.9410.20699.6
4.32-39.8415.4020.14212.96145559519450.980.14899.4

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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: 1.44→39.84 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2000 9.06 %
Rwork0.1905 20081 -
obs0.1934 22081 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.95 Å2 / Biso mean: 25.975 Å2 / Biso min: 13.02 Å2
Refinement stepCycle: final / Resolution: 1.44→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 10 100 1122
Biso mean--29.43 34.65 -
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 (%)
1.44-1.480.33981400.297514161556100
1.48-1.520.28291400.260513971537100
1.52-1.560.2791410.241314121553100
1.56-1.610.2641400.223114091549100
1.61-1.670.29771410.224714201561100
1.67-1.740.23551410.22281403154499
1.74-1.810.23721400.19751404154499
1.81-1.910.22821410.1851417155899
1.91-2.030.22941400.186514151555100
2.03-2.190.25631440.180114461590100
2.19-2.410.2061430.17814351578100
2.41-2.750.24791450.198214571602100
2.75-3.470.221470.18114731620100
3.47-39.840.17891570.178115771734100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8645-0.6691-0.20372.58120.06592.4475-0.0719-0.0665-0.23790.16670.11010.20950.0687-0.2842-0.03850.2519-0.04540.00050.26070.07960.296916.8508-7.18179.0431
24.85470.0866-0.66032.1117-0.44511.2137-0.08010.2549-0.5085-0.0147-0.02880.19810.5674-0.27960.09360.3076-0.0512-0.01060.2072-0.01330.281423.704-11.5963-2.544
31.3093-0.7055-0.02971.2705-0.22970.5748-0.0515-0.11060.10280.04880.0665-0.0614-0.07650.02760.0060.16240.0068-0.00330.17530.02470.173222.08350.58456.076
41.51140.9213-2.05473.198-2.3187.83510.4442-0.07220.3579-0.02280.0117-0.024-0.67610.805-0.33370.2723-0.05020.06150.2455-0.03660.223220.330814.8041-4.6056
51.8505-0.13590.31081.7660.03031.9360.20750.2520.1605-0.296-0.13410.12980.0555-0.0054-0.06360.24240.0233-0.0080.21660.020.189617.56767.7445-7.1072
61.6311-0.30120.39322.6409-0.18091.98890.24850.0025-0.1516-0.4531-0.0560.40820.1989-0.0279-0.13420.25610.0124-0.06260.22410.00240.243312.33623.6388-7.253
73.5904-0.3901-2.22151.71590.16212.62030.01340.261-0.42360.0582-0.06170.26060.3594-0.5324-0.01070.2154-0.0366-0.03280.18-0.00620.232117.6024-4.6681-5.5659
81.9486-0.2365-0.10122.60140.79242.84460.08270.17020.1429-0.1393-0.1159-0.099-0.2830.09290.04950.18040.00150.00030.14820.00440.172530.20430.4672-3.4677
93.70691.3432-2.19642.822-1.5143.4564-0.0934-0.2564-0.47930.3690.1016-0.04030.2805-0.0602-0.03790.24570.023-0.0210.23680.04470.2628.7092-8.378610.7958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )A15 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )A25 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )A43 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )A51 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 88 )A69 - 88
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 99 )A89 - 99
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 114 )A100 - 114
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 129 )A115 - 129

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