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- PDB-7rz2: Hen egg-white lysozyme with ionic liquid ethanolammonium formate ... -

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Basic information

Entry
Database: PDB / ID: 7rz2
TitleHen egg-white lysozyme with ionic liquid ethanolammonium formate 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: 1.07 Å
AuthorsHan, Q. / Darmanin, C. / 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 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 2.1Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6227
Polymers14,3311
Non-polymers2916
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-2 kcal/mol
Surface area6350 Å2
Unit cell
Length a, b, c (Å)76.760, 76.760, 38.560
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
11AAA-333-

HOH

21AAA-341-

HOH

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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.: 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.: 1 / Source method: obtained synthetically / Formula: C2H7NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: ethanolammonium formate 4mol% (ca. 20wt%) 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: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.07→24.29 Å / Num. obs: 50880 / % possible obs: 99.4 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 1.07→1.09 Å / Num. unique obs: 2520 / CC1/2: 0.91 / % 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: 1.07→24.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.778 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1697 2672 5.212 %
Rwork0.152 48595 -
all0.153 --
obs-48595 99.94 %
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: 10.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.07→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 19 123 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0121249
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181178
X-RAY DIFFRACTIONr_angle_refined_deg2.2831.6341709
X-RAY DIFFRACTIONr_angle_other_deg0.8251.5972675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8772078
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1571516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021554
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02360
X-RAY DIFFRACTIONr_nbd_refined0.2590.2280
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2370.21024
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2568
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.267
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3990.215
X-RAY DIFFRACTIONr_nbd_other0.3150.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.211
X-RAY DIFFRACTIONr_mcbond_it2.0230.833613
X-RAY DIFFRACTIONr_mcbond_other1.9850.833612
X-RAY DIFFRACTIONr_mcangle_it2.3951.258792
X-RAY DIFFRACTIONr_mcangle_other2.4131.261792
X-RAY DIFFRACTIONr_scbond_it2.5741.075635
X-RAY DIFFRACTIONr_scbond_other2.5241.067624
X-RAY DIFFRACTIONr_scangle_it3.0931.525909
X-RAY DIFFRACTIONr_scangle_other3.0821.522904
X-RAY DIFFRACTIONr_lrange_it3.25710.2731492
X-RAY DIFFRACTIONr_lrange_other3.1519.9231469
X-RAY DIFFRACTIONr_rigid_bond_restr8.24132425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.0980.1991920.1963545X-RAY DIFFRACTION99.9465
1.098-1.1280.141940.1453454X-RAY DIFFRACTION99.9726
1.128-1.1610.1511640.1233360X-RAY DIFFRACTION99.9716
1.161-1.1960.1211720.1073281X-RAY DIFFRACTION99.971
1.196-1.2350.1441690.1293164X-RAY DIFFRACTION100
1.235-1.2790.1381890.1223064X-RAY DIFFRACTION100
1.279-1.3270.1671680.132958X-RAY DIFFRACTION99.968
1.327-1.3810.1481810.1152820X-RAY DIFFRACTION99.9667
1.381-1.4430.1381310.1112764X-RAY DIFFRACTION100
1.443-1.5130.1661380.1212636X-RAY DIFFRACTION100
1.513-1.5950.1411290.1212519X-RAY DIFFRACTION100
1.595-1.6910.1521650.1182348X-RAY DIFFRACTION100
1.691-1.8080.1511360.1312217X-RAY DIFFRACTION100
1.808-1.9530.1721100.1592118X-RAY DIFFRACTION100
1.953-2.1390.1721050.1531945X-RAY DIFFRACTION99.9512
2.139-2.3910.176960.1631756X-RAY DIFFRACTION99.946
2.391-2.760.178670.1681589X-RAY DIFFRACTION100
2.76-3.3780.239630.1831361X-RAY DIFFRACTION100
3.378-4.7680.171730.1761060X-RAY DIFFRACTION99.9118

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