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- PDB-7rz1: Hen egg-white lysozyme with ionic liquid ethanolammonium formate ... -

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Basic information

Entry
Database: PDB / ID: 7rz1
TitleHen egg-white lysozyme with ionic liquid ethanolammonium formate 14.4 mol%
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / ionic liquid / ethanolammonium formate
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
ETHANOLAMINE / FORMIC ACID / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.046 Å
AuthorsHan, Q. / Darmanin, C. / Drummond, C. / Greaves, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
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 27, 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 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Nov 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)14,6838
Polymers14,3311
Non-polymers3527
Water1,910106
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, The radius of gyration of lysozyme in this solvent increased to over 20 angstrom compared with 15 angstrom in buffer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.650, 76.650, 38.290
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-385-

HOH

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Components

#1: Protein Lysozyme C / lyzozyme / 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe protein is a monomer, but is an oligomer in the presence of concentrated ionic liquid. Under ...The protein is a monomer, but is an oligomer in the presence of concentrated ionic liquid. Under these conditions, SAXS indicates that the radius of gyration increased to over 20 angstroms compared with 15 angstroms in buffer.
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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: ethanolammonium formate 14.4mol% (ca. 50wt%) in water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.046→54.2 Å / Num. obs: 7613 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.981 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.1 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 571 / CC1/2: 0.852 / % 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: 2.046→54.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.14 / SU B: 13.824 / SU ML: 0.156 / Average fsc free: 0.9114 / Average fsc work: 0.9306 / Cross valid method: THROUGHOUT / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2431 390 5.153 %
Rwork0.16 7179 -
all0.164 --
obs-7569 99.435 %
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: 18.825 Å2
Baniso -1Baniso -2Baniso -3
1--1.277 Å20 Å20 Å2
2---1.277 Å20 Å2
3---2.554 Å2
Refinement stepCycle: LAST / Resolution: 2.046→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 23 106 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121118
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181041
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6421512
X-RAY DIFFRACTIONr_angle_other_deg0.5821.5922345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19919.45273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78215184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5461516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021352
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
X-RAY DIFFRACTIONr_nbd_refined0.2240.2277
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.21030
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2534
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.215
X-RAY DIFFRACTIONr_nbd_other0.2430.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_mcbond_it2.1761.59548
X-RAY DIFFRACTIONr_mcbond_other2.0741.581545
X-RAY DIFFRACTIONr_mcangle_it2.8072.384693
X-RAY DIFFRACTIONr_mcangle_other2.8212.389692
X-RAY DIFFRACTIONr_scbond_it3.5141.926570
X-RAY DIFFRACTIONr_scbond_other3.1251.892556
X-RAY DIFFRACTIONr_scangle_it4.1382.769816
X-RAY DIFFRACTIONr_scangle_other3.9832.747809
X-RAY DIFFRACTIONr_lrange_it5.21919.9311388
X-RAY DIFFRACTIONr_lrange_other4.6519.4081357
X-RAY DIFFRACTIONr_rigid_bond_restr2.58832158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.046-2.0990.295240.2125200.2155440.8310.8871000.194
2.099-2.1570.221190.2125110.2125300.910.8511000.18
2.157-2.2190.286300.2184960.2225260.8170.8251000.182
2.219-2.2870.473250.3364430.3435050.790.88292.67330.305
2.287-2.3620.335250.1864630.1964880.880.8841000.15
2.362-2.4450.2290.1354450.1394740.9230.9441000.107
2.445-2.5370.233250.1364380.1434630.9350.9491000.112
2.537-2.640.285270.1184170.1274440.9210.9561000.097
2.64-2.7580.18180.1184220.1214400.9590.9591000.097
2.758-2.8920.193160.1043730.1073890.9490.9661000.087
2.892-3.0480.235220.1163730.1223950.9380.9691000.103
3.048-3.2320.283160.1363630.1413790.9120.9681000.124
3.232-3.4540.136140.153380.1493520.9620.9731000.141
3.454-3.730.205190.143110.1443330.950.97399.09910.13
3.73-4.0840.182160.1222870.1253060.9580.97599.01960.112
4.084-4.5630.183140.1242600.1272740.9690.9781000.117
4.563-5.2620.229180.1562370.1632550.9650.9761000.146
5.262-6.430.229160.1882070.1912230.960.9711000.167
6.43-9.030.252110.1851650.1891760.9440.971000.172
9.03-54.20.34260.2291100.2331160.9450.9581000.222
Refinement TLS params.Method: refined / Origin x: -19.5967 Å / Origin y: -1.6795 Å / Origin z: -9.3171 Å
111213212223313233
T0.0036 Å20.0005 Å20.0002 Å2-0.0042 Å20.0078 Å2--0.0275 Å2
L0.7343 °20.3213 °2-0.0667 °2-0.6427 °20.2829 °2--0.3586 °2
S-0.0243 Å °-0.0369 Å °-0.0501 Å °-0.0271 Å °0.0045 Å °-0.033 Å °0.0074 Å °0.0248 Å °0.0198 Å °
Refinement TLS groupSelection: ALL

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