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- PDB-7ryd: Hen egg-white lysozyme with ionic liquid butylammonium nitrate 1 mol% -

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Basic information

Entry
Database: PDB / ID: 7ryd
TitleHen egg-white lysozyme with ionic liquid butylammonium nitrate 1 mol%
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / ionic liquid / butylammonium 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 Gram-positive 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 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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,40614
Polymers28,6622
Non-polymers74412
Water3,117173
1
AAA: Lysozyme C
hetero molecules


  • defined by author
  • 14.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,8279
Polymers14,3311
Non-polymers4968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Lysozyme C
hetero molecules


  • defined by author
  • 14.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,5795
Polymers14,3311
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.640, 62.450, 59.780
Angle α, β, γ (deg.)90.000, 90.210, 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 / Nitrate


Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.8 Å3/Da / Density % sol: 31.67 %
Crystal growTemperature: 298.15 K / Method: microbatch / pH: 8 / Details: butylammonium nitrate 1 mol% (ca. 7wt%) 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: 1.18→43.18 Å / Num. obs: 67030 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.992 / Net I/σ(I): 5.4
Reflection shellResolution: 1.18→1.2 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3344 / CC1/2: 0.036 / % possible all: 99.6

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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: 1.18→17.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.799 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.22994 3100 4.9 %
Rwork0.19908 59883 -
obs-59883 93.68 %
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: 14.338 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0.069 Å2
2---0.359 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.18→17.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 48 173 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181913
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.6362970
X-RAY DIFFRACTIONr_angle_other_deg1.6571.5894417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9315276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.88919.925134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0771527
X-RAY DIFFRACTIONr_chiral_restr0.1060.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022585
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02540
X-RAY DIFFRACTIONr_nbd_refined0.2280.2483
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21801
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21083
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.234
X-RAY DIFFRACTIONr_nbd_other0.2390.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.222
X-RAY DIFFRACTIONr_mcbond_it2.1961.2831079
X-RAY DIFFRACTIONr_mcbond_other2.1711.2791078
X-RAY DIFFRACTIONr_mcangle_it2.5771.9311361
X-RAY DIFFRACTIONr_mcangle_other2.5791.9351362
X-RAY DIFFRACTIONr_scbond_it3.0931.6271115
X-RAY DIFFRACTIONr_scbond_other2.9951.6091104
X-RAY DIFFRACTIONr_scangle_it3.7262.3161607
X-RAY DIFFRACTIONr_scangle_other3.6332.2961596
X-RAY DIFFRACTIONr_lrange_it3.70815.8682651
X-RAY DIFFRACTIONr_lrange_other3.64515.6422618
X-RAY DIFFRACTIONr_rigid_bond_restr2.93234107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.2070.4112240.434734X-RAY DIFFRACTION99.6783
1.207-1.2410.3912390.3924567X-RAY DIFFRACTION99.8753
1.241-1.2760.3482370.3574438X-RAY DIFFRACTION99.9359
1.276-1.3160.3461850.3184438X-RAY DIFFRACTION100
1.316-1.3590.332010.2854161X-RAY DIFFRACTION99.9771
1.359-1.4070.2762000.2384071X-RAY DIFFRACTION99.9766
1.407-1.460.2531910.2053340X-RAY DIFFRACTION84.3325
1.46-1.5190.2221760.1563134X-RAY DIFFRACTION84.0315
1.519-1.5870.2341260.1523082X-RAY DIFFRACTION84.4878
1.587-1.6640.1991970.1293456X-RAY DIFFRACTION100
1.664-1.7540.1821820.1223292X-RAY DIFFRACTION100
1.754-1.860.1911590.1193144X-RAY DIFFRACTION100
1.86-1.9890.193770.1181747X-RAY DIFFRACTION58.9909
1.989-2.1480.1851150.1252467X-RAY DIFFRACTION89.6839
2.148-2.3520.1681510.1222181X-RAY DIFFRACTION87.9668
2.352-2.630.1961560.1312243X-RAY DIFFRACTION100
2.63-3.0350.16930.141895X-RAY DIFFRACTION93.3772
3.035-3.7150.204830.1451551X-RAY DIFFRACTION90.7274
3.715-5.2440.166750.1371229X-RAY DIFFRACTION93.01

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