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- PDB-8aj3: X-ray structure of lysozyme obtained upon reaction with [VIVO(mal... -

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Basic information

Entry
Database: PDB / ID: 8aj3
TitleX-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (Structure A)
ComponentsLysozyme
KeywordsHYDROLASE / metallodrug / vanadium / oxidovanadium / covalent binding / non-covalent binding / protein-metal interaction
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 / Chem-MKO / Chem-MNW / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsPaolillo, M. / Merlino, A. / Ferraro, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Inorg.Chem. / Year: 2022
Title: Multiple and Variable Binding of Pharmacologically Active Bis(maltolato)oxidovanadium(IV) to Lysozyme.
Authors: Ferraro, G. / Paolillo, M. / Sciortino, G. / Garribba, E. / Merlino, A.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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)15,3066
Polymers14,3311
Non-polymers9745
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.890, 76.890, 38.050
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-326-

HOH

21A-346-

HOH

31A-423-

HOH

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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

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Non-polymers , 6 types, 163 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: 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
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MKO / 8,8-bis($l^{1}-oxidanyl)-2,2'-dimethyl-8,8'-spirobi[3$l^{4},7,9-trioxa-8$l^{6}-vanadabicyclo[4.3.0]nona-1(6),2,4-triene]


Mass: 333.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O8V / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MNW / 8,8,8,8-tetrakis($l^{1}-oxidanyl)-2-methyl-3,7,9-trioxa-8$l^{6}-vanadabicyclo[4.3.0]nona-1,5-diene


Mass: 244.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9O7V / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 2.0 M sodium formate and 0.1 M Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→54.37 Å / Num. obs: 42289 / % possible obs: 97.3 % / Redundancy: 16.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.4
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1866 / CC1/2: 0.926 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.13→54.369 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.438 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.051
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2493 2091 4.96 %
Rwork0.1994 40065 -
all0.202 --
obs-42156 97.464 %
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: 16.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.855 Å20 Å20 Å2
2---0.855 Å20 Å2
3---1.709 Å2
Refinement stepCycle: LAST / Resolution: 1.13→54.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 57 158 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121121
X-RAY DIFFRACTIONr_ext_dist_refined_d0.010.011
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.5751525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19520.80662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34815179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8881511
X-RAY DIFFRACTIONr_chiral_restr0.1290.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02872
X-RAY DIFFRACTIONr_nbd_refined0.220.2599
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2103
X-RAY DIFFRACTIONr_metal_ion_refined0.2420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2790.225
X-RAY DIFFRACTIONr_mcbond_it2.0141.186530
X-RAY DIFFRACTIONr_mcangle_it2.3221.782666
X-RAY DIFFRACTIONr_scbond_it3.0671.52591
X-RAY DIFFRACTIONr_scangle_it3.5322.187859
X-RAY DIFFRACTIONr_lrange_it3.97818.741883
X-RAY DIFFRACTIONr_rigid_bond_restr6.46531121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.13-1.1590.2691430.2327620.23231550.9310.93192.07610.212
1.159-1.1910.3361460.31927700.31930590.7850.85695.32530.291
1.191-1.2260.3431360.29927740.30129920.8240.88697.25940.284
1.226-1.2630.4891040.42226070.42528960.5850.63593.61190.389
1.263-1.3050.3331300.3425530.3428120.6980.72495.41250.301
1.305-1.350.2491320.18825770.19127210.8870.89499.5590.162
1.35-1.4010.4031370.29223470.29926290.7410.81594.48460.249
1.401-1.4590.2271340.19123790.19325500.820.89298.5490.171
1.459-1.5230.3391290.24722610.25224420.7690.85597.87060.217
1.523-1.5980.2041220.1522010.15223410.9270.94299.23110.137
1.598-1.6840.2031180.10421070.10822250.950.9751000.104
1.684-1.7860.1771100.12119910.12421190.960.97199.15050.124
1.786-1.9090.1971000.14518880.14720000.9370.9699.40.151
1.909-2.0620.245890.2117570.21218480.8940.92999.89180.203
2.062-2.2590.284950.23516610.23817560.8850.9141000.221
2.259-2.5250.201650.1614940.16115600.9470.94899.93590.189
2.525-2.9140.214710.16113230.16413950.9480.95899.92830.194
2.914-3.5660.204680.14911360.15212050.9560.96699.9170.194
3.566-5.0330.179390.1489170.1499570.9630.97599.89550.191
5.033-54.3690.318230.2865520.2875810.9220.9498.96730.369

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