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Basic information

Entry
Database: PDB / ID: 8pte
TitlePolyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to octadecavanadate ion (structure B)
ComponentsLysozyme C
KeywordsHYDROLASE / protein interaction / vanadium / vanadium acetylacetonate / POV / polyoxo
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
pentakis(oxidanyl)vanadium / Polyoxidovanadate complex / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsTito, G. / Ferraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Stabilization and Binding of [V 4 O 12 ] 4- and Unprecedented [V 20 O 54 (NO 3 )] n- to Lysozyme upon Loss of Ligands and Oxidation of the Potential Drug V IV O(acetylacetonato) 2.
Authors: Ferraro, G. / Tito, G. / Sciortino, G. / Garribba, E. / Merlino, A.
History
DepositionJul 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)16,5597
Polymers14,3311
Non-polymers2,2286
Water2,792155
1
AAA: Lysozyme C
hetero molecules

AAA: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,11814
Polymers28,6622
Non-polymers4,45612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)80.390, 80.390, 36.510
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-206-

NO3

21AAA-352-

HOH

31AAA-453-

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 , 5 types, 161 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-JQJ / Polyoxidovanadate complex


Mass: 1882.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O54V20 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-H1W / pentakis(oxidanyl)vanadium


Mass: 135.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O5V / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% ethylene glycol, 0.1 M sodium acetate buffer pH 4.0, 0.6 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.79→40.19 Å / Num. obs: 11611 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.104 / Net I/σ(I): 33.6
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 15 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 576 / CC1/2: 0.912 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.797→40.128 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.769 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2325 580 5.089 %
Rwork0.1805 10818 -
all0.183 --
obs-11398 97.938 %
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: 26.962 Å2
Baniso -1Baniso -2Baniso -3
1--0.219 Å20 Å20 Å2
2---0.219 Å20 Å2
3---0.438 Å2
Refinement stepCycle: LAST / Resolution: 1.797→40.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 56 155 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0141142
X-RAY DIFFRACTIONr_bond_other_d0.0010.014995
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.7111569
X-RAY DIFFRACTIONr_angle_other_deg1.4151.5972267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7920.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36715180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1571514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021325
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02311
X-RAY DIFFRACTIONr_nbd_refined0.2410.2270
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.2947
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2530
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.282
X-RAY DIFFRACTIONr_metal_ion_refined0.2320.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.224
X-RAY DIFFRACTIONr_nbd_other0.1880.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0480.21
X-RAY DIFFRACTIONr_mcbond_it2.292.438540
X-RAY DIFFRACTIONr_mcbond_other2.2532.426539
X-RAY DIFFRACTIONr_mcangle_it3.233.631682
X-RAY DIFFRACTIONr_mcangle_other3.2433.644683
X-RAY DIFFRACTIONr_scbond_it2.9742.873602
X-RAY DIFFRACTIONr_scbond_other2.9952.88545
X-RAY DIFFRACTIONr_scangle_it4.6514.138880
X-RAY DIFFRACTIONr_scangle_other4.8174.161794
X-RAY DIFFRACTIONr_lrange_it7.15729.9111351
X-RAY DIFFRACTIONr_lrange_other6.78629.0371304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.797-1.8440.434400.353641X-RAY DIFFRACTION81.2649
1.844-1.8940.314320.286715X-RAY DIFFRACTION91.9951
1.894-1.9490.308340.238754X-RAY DIFFRACTION99.4949
1.949-2.0090.263440.212738X-RAY DIFFRACTION99.7449
2.009-2.0740.241380.2690X-RAY DIFFRACTION100
2.074-2.1470.227400.189714X-RAY DIFFRACTION100
2.147-2.2280.199460.178649X-RAY DIFFRACTION100
2.228-2.3180.232260.18656X-RAY DIFFRACTION99.4169
2.318-2.4210.228410.178616X-RAY DIFFRACTION99.848
2.421-2.5390.271340.174585X-RAY DIFFRACTION99.8387
2.539-2.6760.227250.179574X-RAY DIFFRACTION99.8333
2.676-2.8370.311260.178539X-RAY DIFFRACTION99.8233
2.837-3.0320.306310.185512X-RAY DIFFRACTION100
3.032-3.2730.269200.146481X-RAY DIFFRACTION99.8008
3.273-3.5830.226210.159444X-RAY DIFFRACTION100
3.583-4.0020.185220.148413X-RAY DIFFRACTION99.7706
4.002-4.6140.14230.134359X-RAY DIFFRACTION100
4.614-5.6320.199160.171312X-RAY DIFFRACTION100
5.632-7.8880.167120.179259X-RAY DIFFRACTION100
7.888-100.26290.239164X-RAY DIFFRACTION100

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