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- PDB-7jmu: Hen egg-white lysozyme with ionic liquid ethylammonium nitrate -

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Basic information

Entry
Database: PDB / ID: 7jmu
TitleHen egg-white lysozyme with ionic liquid ethylammonium nitrate
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / ionic liquid / 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: 1.2 Å
AuthorsHan, Q. / Darmanin, C. / Smith, K. / Greaves, T. / Drummond, C.
CitationJournal: J Colloid Interface Sci / Year: 2021
Title: Lysozyme conformational changes with ionic liquids: Spectroscopic, small angle x-ray scattering and crystallographic study.
Authors: Han, Q. / Smith, K.M. / Darmanin, C. / Ryan, T.M. / Drummond, C.J. / Greaves, T.L.
History
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,59217
Polymers28,6622
Non-polymers93015
Water4,540252
1
A: 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
MethodPISA
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8279
Polymers14,3311
Non-polymers4968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.585, 62.637, 59.645
Angle α, β, γ (deg.)90.000, 90.540, 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) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 31.58 %
Crystal growTemperature: 298.15 K / Method: batch mode / pH: 8 / Details: 5.7% w/v ethylammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953646 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953646 Å / Relative weight: 1
ReflectionResolution: 1.2→43.19 Å / Num. obs: 60488 / % possible obs: 95.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 19.5 / Num. measured all: 417805 / Scaling rejects: 60
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.2260.3451575426310.9380.1520.3783.985.2
6.57-43.196.70.02927094060.9990.0120.0315499.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DPW

1dpw


Resolution: 1.2→29.82 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.543 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1827 2781 4.6 %RANDOM
Rwork0.1475 ---
obs0.149 57703 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 15.044 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.02 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.2→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 60 254 2313
Biso mean--27.24 24.3 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132176
X-RAY DIFFRACTIONr_bond_other_d0.0090.0181870
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.6352947
X-RAY DIFFRACTIONr_angle_other_deg1.791.5874320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83920.611131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47815344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8961524
X-RAY DIFFRACTIONr_chiral_restr0.130.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022574
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02522
X-RAY DIFFRACTIONr_rigid_bond_restr7.05634046
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 155 -
Rwork0.19 3833 -
all-3988 -
obs--86.47 %

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