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- PDB-7yrk: Crystal structure of the hen egg lysozyme-2-oxidobenzylidene-thre... -

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Basic information

Entry
Database: PDB / ID: 7yrk
TitleCrystal structure of the hen egg lysozyme-2-oxidobenzylidene-threoninato-copper (II) complex
ComponentsLysozyme C
KeywordsHYDROLASE / complex / enzyme / lysozyme / activity
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
methyl radical / Chem-JI6 / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsUnno, M. / Furuya, T. / Kitanishi, K. / Akitsu, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00336 Japan
CitationJournal: Sci Rep / Year: 2023
Title: A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme.
Authors: Furuya, T. / Nakane, D. / Kitanishi, K. / Katsuumi, N. / Tsaturyan, A. / Shcherbakov, I.N. / Unno, M. / Akitsu, T.
History
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,89212
Polymers16,2581
Non-polymers63511
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.671, 78.671, 37.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-208-

NA

21A-374-

HOH

31A-512-

HOH

41A-535-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 16257.660 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, 246 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-JI6 / (6~{S})-6-[(1~{R})-1-oxidanylethyl]-2,4-dioxa-7$l^{4}-aza-3$l^{3}-cupratricyclo[7.4.0.0^{3,7}]trideca-1(13),7,9,11-tetraen-5-one


Mass: 284.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11CuNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-74C / methyl radical


Mass: 15.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 1.77 Å3/Da / Density % sol: 30.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M of acetic acid-sodium acetate buffer (pH 4.7) including 2-6 % (m/v) of NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.92→35.18 Å / Num. obs: 78748 / % possible obs: 98.2 % / Redundancy: 11.6 % / Biso Wilson estimate: 8.26 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 17
Reflection shellResolution: 0.92→0.94 Å / Rmerge(I) obs: 0.568 / Num. unique obs: 2783

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LYT

5lyt


Resolution: 0.92→35.18 Å / SU ML: 0.0597 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.2891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1284 7868 10 %
Rwork0.1126 70811 -
obs0.1142 78679 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.05 Å2
Refinement stepCycle: LAST / Resolution: 0.92→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 33 235 1269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071189
X-RAY DIFFRACTIONf_angle_d1.15191634
X-RAY DIFFRACTIONf_chiral_restr0.0979170
X-RAY DIFFRACTIONf_plane_restr0.0134215
X-RAY DIFFRACTIONf_dihedral_angle_d6.4501190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.930.2331650.2311479X-RAY DIFFRACTION62.16
0.93-0.950.19762410.16842171X-RAY DIFFRACTION91.64
0.95-0.960.15512520.15082275X-RAY DIFFRACTION95.04
0.96-0.970.15562550.13382294X-RAY DIFFRACTION97.29
0.97-0.980.13242550.12572299X-RAY DIFFRACTION97.56
0.98-0.990.16012660.14292385X-RAY DIFFRACTION100
1-1.010.12292610.10732350X-RAY DIFFRACTION99.54
1.01-1.020.12432640.09682376X-RAY DIFFRACTION100
1.02-1.040.13032650.10912388X-RAY DIFFRACTION99.85
1.04-1.060.12052650.09942381X-RAY DIFFRACTION100
1.06-1.080.10192630.09422368X-RAY DIFFRACTION99.92
1.08-1.10.09472670.09182405X-RAY DIFFRACTION100
1.1-1.120.10862640.09112379X-RAY DIFFRACTION100
1.12-1.140.11862640.09982373X-RAY DIFFRACTION100
1.14-1.160.09232670.09212399X-RAY DIFFRACTION100
1.16-1.190.09382660.08822394X-RAY DIFFRACTION100
1.19-1.220.1032630.0852362X-RAY DIFFRACTION100
1.22-1.250.10072660.08642396X-RAY DIFFRACTION99.92
1.25-1.290.10062670.09042421X-RAY DIFFRACTION99.96
1.29-1.330.11222660.08982395X-RAY DIFFRACTION99.96
1.33-1.380.11862690.09692414X-RAY DIFFRACTION99.96
1.38-1.430.11112660.09322394X-RAY DIFFRACTION100
1.44-1.50.10392680.09122413X-RAY DIFFRACTION99.96
1.5-1.580.09282680.09342408X-RAY DIFFRACTION100
1.58-1.680.11232690.09712430X-RAY DIFFRACTION100
1.68-1.810.12932700.11032426X-RAY DIFFRACTION100
1.81-1.990.1232730.11112456X-RAY DIFFRACTION100
1.99-2.280.13482730.11472458X-RAY DIFFRACTION99.93
2.28-2.870.14712780.12542500X-RAY DIFFRACTION100
2.87-35.180.15872920.14142622X-RAY DIFFRACTION99.52

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