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- PDB-7rxy: Hen egg-white lysozyme with ionic liquid ethylammonium nitrate 5 mol% -

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Basic information

Entry
Database: PDB / ID: 7rxy
TitleHen egg-white lysozyme with ionic liquid ethylammonium nitrate 5 mol%
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / ionic liquid / ethylammonium nitrate
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive bacterium / endoplasmic reticulum / : / 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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHan, Q. / Darmanin, C. / Smith, K. / Drummond, C. / Greaves, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Colloid Interface Sci / Year: 2023
Title: Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids.
Authors: Han, Q. / Su, Y. / Smith, K.M. / Binns, J. / Drummond, C.J. / Darmanin, C. / Greaves, T.L.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
AAA: Lysozyme C
BBB: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,46815
Polymers28,6622
Non-polymers80613
Water2,594144
1
AAA: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7658
Polymers14,3311
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7037
Polymers14,3311
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.531, 62.477, 59.648
Angle α, β, γ (deg.)90.000, 90.262, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.79 Å3/Da / Density % sol: 31.28 %
Crystal growTemperature: 293.15 K / Method: microbatch
Details: ionic liquid ethylammonium nitrate 5 mol% (ca. 24wt%) in water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→43.14 Å / Num. obs: 26661 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.999 / Net I/σ(I): 10.1
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1365 / CC1/2: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMU

7jmu


Resolution: 1.6→29.841 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.149 / SU B: 4.456 / SU ML: 0.07 / Average fsc free: 0.9323 / Average fsc work: 0.9538 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.207 1352 5.178 %
Rwork0.1397 24759 -
all0.143 --
obs-26111 97.713 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.154 Å2-0 Å2-0.706 Å2
2--0.163 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 52 144 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122141
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.632891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0855266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.22120.076131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43515347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2561526
X-RAY DIFFRACTIONr_chiral_restr0.10.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021714
X-RAY DIFFRACTIONr_nbd_refined0.2080.21019
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21433
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2126
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.216
X-RAY DIFFRACTIONr_mcbond_it3.9242.1221049
X-RAY DIFFRACTIONr_mcangle_it4.7783.1921314
X-RAY DIFFRACTIONr_scbond_it5.3472.6141092
X-RAY DIFFRACTIONr_scangle_it5.6623.7391575
X-RAY DIFFRACTIONr_lrange_it5.75330.1393391
X-RAY DIFFRACTIONr_rigid_bond_restr5.45732141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2811070.1491794X-RAY DIFFRACTION97.5372
1.642-1.6860.209840.1411768X-RAY DIFFRACTION97.5764
1.686-1.7350.205880.1241779X-RAY DIFFRACTION97.7487
1.735-1.7890.228710.1271667X-RAY DIFFRACTION97.8604
1.789-1.8470.2561050.1371645X-RAY DIFFRACTION97.82
1.847-1.9120.2511000.1371522X-RAY DIFFRACTION97.7697
1.912-1.9840.289840.1261553X-RAY DIFFRACTION98.1415
1.984-2.0650.192820.121461X-RAY DIFFRACTION98.2803
2.065-2.1570.206800.1211406X-RAY DIFFRACTION97.8275
2.157-2.2620.19570.1261379X-RAY DIFFRACTION98.8981
2.262-2.3840.206770.1371266X-RAY DIFFRACTION98.1725
2.384-2.5280.247610.1351251X-RAY DIFFRACTION98.4246
2.528-2.7030.2520.141145X-RAY DIFFRACTION98.1952
2.703-2.9190.219600.1391056X-RAY DIFFRACTION98.0668
2.919-3.1970.251400.15974X-RAY DIFFRACTION96.5714
3.197-3.5730.195490.139878X-RAY DIFFRACTION96.9665
3.573-4.1230.177700.132760X-RAY DIFFRACTION96.3995
4.123-5.0430.159420.141662X-RAY DIFFRACTION97.5069
5.043-7.1070.24200.174513X-RAY DIFFRACTION95.3488

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