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- PDB-9gog: X-ray structure of lysozyme obtained upon reaction with the dioxi... -

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Basic information

Entry
Database: PDB / ID: 9gog
TitleX-ray structure of lysozyme obtained upon reaction with the dioxidovanadium(V) complex with furan-2-carboxylic acid (3-ethoxy-2-hydroxybenzylidene)hydrazide
ComponentsLysozyme C
KeywordsHYDROLASE / metallodrugs / protein metalation / vanadium compounds / protein metal compounds interactions
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 / bis(oxidanyl)vanadium / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsPaolillo, M. / Ferraro, G. / Merlino, A.
Funding support Italy, India, 3items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2022JMFC3X Italy
Council of Scientific & Industrial Research (CSIR)01(3073)/21/EMR-II India
Science and Engineering Research Board (SERB)CRG/2023/000884 India
CitationJournal: J.Inorg.Biochem. / Year: 2024
Title: Interaction of V V O 2 -hydrazonates with lysozyme.
Authors: Paolillo, M. / Ferraro, G. / Sahu, G. / Pattanayak, P.D. / Garribba, E. / Halder, S. / Ghosh, R. / Mondal, B. / Chatterjee, P.B. / Dinda, R. / Merlino, A.
History
DepositionSep 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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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)15,3269
Polymers14,3311
Non-polymers9958
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-27 kcal/mol
Surface area6740 Å2
Unit cell
Length a, b, c (Å)76.846, 76.846, 36.839
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-336-

HOH

21AAA-337-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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

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Non-polymers , 6 types, 114 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-VVB / bis(oxidanyl)vanadium


Mass: 84.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2V / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-A1IOM / dioxidovanadium(V) complex with furan-2-carboxylic acid (3-ethoxy-2-hydroxybenzylidene)hydrazide / 13-ethoxy-5-(furan-2-yl)-2,4$l^{3}-dioxa-6,7$l^{4}-diaza-3$l^{7}-vanadatricyclo[7.4.0.0^{3,7}]trideca-1(9),4,7,10,12-pentaene 3,3-dioxide


Mass: 355.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O6V
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.24→54.34 Å / Num. obs: 32110 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 1555 / CC1/2: 0.412

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→54.338 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.339 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2559 1554 4.894 %
Rwork0.203 30200 -
all0.205 --
obs-31754 99.689 %
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: 24.679 Å2
Baniso -1Baniso -2Baniso -3
1-0.095 Å2-0 Å2-0 Å2
2--0.095 Å2-0 Å2
3----0.191 Å2
Refinement stepCycle: LAST / Resolution: 1.24→54.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 60 106 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131165
X-RAY DIFFRACTIONr_bond_other_d0.0020.0141037
X-RAY DIFFRACTIONr_angle_refined_deg1.861.6951577
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5982369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22220.29967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95315191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3091513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021370
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02306
X-RAY DIFFRACTIONr_nbd_refined0.250.2282
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2966
X-RAY DIFFRACTIONr_nbtor_refined0.180.2560
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.271
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.216
X-RAY DIFFRACTIONr_nbd_other0.2210.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2490.217
X-RAY DIFFRACTIONr_mcbond_it2.1592.284551
X-RAY DIFFRACTIONr_mcbond_other2.1572.273548
X-RAY DIFFRACTIONr_mcangle_it2.963.425695
X-RAY DIFFRACTIONr_mcangle_other2.9583.429696
X-RAY DIFFRACTIONr_scbond_it2.7282.773613
X-RAY DIFFRACTIONr_scbond_other2.6382.604560
X-RAY DIFFRACTIONr_scangle_it4.2954.002882
X-RAY DIFFRACTIONr_scangle_other4.1913.784816
X-RAY DIFFRACTIONr_lrange_it5.67729.2671649
X-RAY DIFFRACTIONr_lrange_other5.44627.3791347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.2720.4851290.4642102X-RAY DIFFRACTION95.7511
1.272-1.3070.3931070.3932133X-RAY DIFFRACTION100
1.307-1.3450.3111120.3112075X-RAY DIFFRACTION100
1.345-1.3860.3261210.3262016X-RAY DIFFRACTION100
1.386-1.4320.346860.2781981X-RAY DIFFRACTION100
1.432-1.4820.2661000.2571914X-RAY DIFFRACTION100
1.482-1.5380.2591000.2341848X-RAY DIFFRACTION100
1.538-1.6010.322890.2321781X-RAY DIFFRACTION100
1.601-1.6720.263730.2291725X-RAY DIFFRACTION100
1.672-1.7530.286760.2321642X-RAY DIFFRACTION100
1.753-1.8480.296880.2271557X-RAY DIFFRACTION100
1.848-1.960.249800.2081462X-RAY DIFFRACTION100
1.96-2.0950.246650.1951405X-RAY DIFFRACTION100
2.095-2.2630.272690.1951313X-RAY DIFFRACTION100
2.263-2.4780.21620.1811216X-RAY DIFFRACTION100
2.478-2.770.241440.1831106X-RAY DIFFRACTION100
2.77-3.1970.267530.194989X-RAY DIFFRACTION100
3.197-3.9120.233510.159835X-RAY DIFFRACTION100
3.912-5.5180.189210.164691X-RAY DIFFRACTION100
5.518-54.3380.264280.256407X-RAY DIFFRACTION100

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