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- PDB-30jx: X-ray structure of lysozyme treated with V(V)-lactate complex (st... -

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Basic information

Entry
Database: PDB / ID: 30jx
TitleX-ray structure of lysozyme treated with V(V)-lactate complex (structure C)
ComponentsLysozyme C
KeywordsHYDROLASE / protein metalation
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive bacterium / Golgi apparatus / endoplasmic reticulum / : / 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
: / : / oxovanadium(2+) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.524 Å
AuthorsPaolillo, M. / Ferraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2022JMFC3X Italy
CitationJournal: Inorg.Chem. / Year: 2026
Title: Speciation, Protein Binding, Biotransformation, and Cytotoxicity of a VV-Lactate Complex.
Authors: Paolillo, M. / Cuomo, V. / Ferraro, G. / Imbimbo, P. / Gumerova, N.I. / Pisanu, F. / Garribba, E. / Rompel, A. / Merlino, A.
History
DepositionApr 29, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: 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)15,2485
Polymers14,3311
Non-polymers9174
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.399, 76.399, 37.012
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-318-

HOH

21AAA-330-

HOH

31AAA-408-

HOH

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Components

#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
#2: Chemical ChemComp-A1J62 / Trinuclear vanadium-lactate complex


Mass: 440.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O13V3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1J6T / Dioxidovanadium(V) lactate complex / (5~{S},10~{S})-5,10-dimethyl-2,2,7,7-tetrakis(oxidanylidene)-1$l^{3},3,6$l^{3},8-tetraoxa-2$l^{7},7$l^{7}-divanadatricyclo[5.3.0.0^{2,6}]decane-4,9-dione


Mass: 342.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O10V2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M succinic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.49→54.01 Å / Num. obs: 18528 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.996 / Net I/σ(I): 7.7
Reflection shellResolution: 1.49→1.51 Å / Num. unique obs: 893 / CC1/2: 0.398

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.524→54.006 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.983 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2271 801 5.005 %
Rwork0.1755 15203 -
all0.178 --
obs-16004 92.653 %
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: 22.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.076 Å20 Å20 Å2
2---0.076 Å20 Å2
3---0.151 Å2
Refinement stepCycle: LAST / Resolution: 1.524→54.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 44 110 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121089
X-RAY DIFFRACTIONr_bond_other_d0.0010.014960
X-RAY DIFFRACTIONr_angle_refined_deg4.1571.7451494
X-RAY DIFFRACTIONr_angle_other_deg1.4771.5962190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10220.80662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60115172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8361511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined0.2280.2222
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.2895
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2508
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.214
X-RAY DIFFRACTIONr_nbd_other0.1960.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.229
X-RAY DIFFRACTIONr_mcbond_it2.1712.088520
X-RAY DIFFRACTIONr_mcbond_other2.1542.082519
X-RAY DIFFRACTIONr_mcangle_it3.3353.124650
X-RAY DIFFRACTIONr_mcangle_other3.3433.13651
X-RAY DIFFRACTIONr_scbond_it3.142.538568
X-RAY DIFFRACTIONr_scbond_other3.0252.456522
X-RAY DIFFRACTIONr_scangle_it4.8333.702840
X-RAY DIFFRACTIONr_scangle_other4.8093.548764
X-RAY DIFFRACTIONr_lrange_it6.66325.2421227
X-RAY DIFFRACTIONr_lrange_other6.59424.721203
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
1.524-1.5640.321220.3032770.30512550.7510.81323.82470.302
1.564-1.6060.245460.2799100.27812170.8430.83678.55380.277
1.606-1.6530.31510.25410750.25611700.8570.86596.23930.251
1.653-1.7040.272550.24110950.24211510.8510.88199.91310.226
1.704-1.760.23630.2210670.22111300.9130.9091000.205
1.76-1.8210.304590.20110220.20610810.8720.9281000.181
1.821-1.890.23630.1859850.18810480.9270.9361000.169
1.89-1.9670.239430.1819770.18310200.9130.9391000.164
1.967-2.0540.222470.1749180.1769650.9320.9461000.161
2.054-2.1550.242490.168880.1649370.9360.9581000.153
2.155-2.2710.206380.1538370.1558760.950.96799.88580.151
2.271-2.4080.23390.1548120.1588510.9460.961000.157
2.408-2.5740.18370.1687690.1698060.9590.9581000.175
2.574-2.780.185400.1557030.1577430.9620.9651000.167
2.78-3.0450.211300.1726700.1737000.9440.9611000.192
3.045-3.4030.203330.1626010.1646340.9540.9661000.19
3.403-3.9260.176260.145290.1425550.9650.9731000.169
3.926-4.8020.171280.1334670.1354960.9680.97699.79840.172
4.802-6.7650.294220.2023670.2073890.9330.951000.271
6.765-54.0060.45100.2692340.2772460.8530.91199.1870.336

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