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- PDB-7b9j: Lysozyme crystallized in the presence of the hydrated deep eutect... -

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Basic information

Entry
Database: PDB / ID: 7b9j
TitleLysozyme crystallized in the presence of the hydrated deep eutectic solvent Choline chloride-Urea 1:2
ComponentsLysozyme
KeywordsHYDROLASE / complex / lysozyme / hydrated deep eutectic solvents
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
ACETATE ION / CHOLINE ION / UREA / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBelviso, B.D. / Caliandro, R. / Carrozzini, B.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
European Commission712965European Union
Italian Ministry of Education2017 A5HXFC_002 Italy
CitationJournal: Acs Sustain Chem Eng / Year: 2021
Title: Introducing Protein Crystallization in Hydrated Deep Eutectic Solvents
Authors: Belviso, B.D. / Perna, F.M. / Carrozzini, B. / Trotta, M. / Capriati, V. / Caliandro, R.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,41526
Polymers14,3311
Non-polymers1,08325
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-149 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.050, 80.050, 36.769
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-215-

CL

21A-222-

URE

31A-222-

URE

41A-223-

URE

51A-223-

URE

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 6 types, 125 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: sodium chloride, sodium acetate, DES: Choline chloride/Urea

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 293 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→56.604 Å / Num. obs: 6448 / % possible obs: 99.9 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.029 / Rrim(I) all: 0.145 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.263 Å / Redundancy: 26.2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 496 / CC1/2: 0.983 / Rpim(I) all: 0.116 / Rrim(I) all: 0.59 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
Sir2014phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n9r

4n9r


Resolution: 2.2→56.604 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 296 4.59 %
Rwork0.1782 6148 -
obs0.1804 6444 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.45 Å2 / Biso mean: 21.9748 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 2.2→56.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 52 100 1153
Biso mean--28.9 27.36 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2003-2.2630.2581550.18632981
2.7721-56.6040.20811410.17473167

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