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- PDB-9rbg: X-ray structure of decavanadate/lysozyme adduct obtained when the... -

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Basic information

Entry
Database: PDB / ID: 9rbg
TitleX-ray structure of decavanadate/lysozyme adduct obtained when the protein is treated with Cs2[V(V)2O4(mal)2]2H2O (structure A)
ComponentsLysozyme C
KeywordsHYDROLASE / Vanadium compounds / decavanadate / lysozyme / 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 / 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
: / DECAVANADATE / oxovanadium(2+) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsPaolillo, M. / Ferraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Inorg Chem Front / Year: 2025
Title: Speciation and structural transformation of a V V -malate complex in the absence and in the presence of a protein: from a dinuclear species to decavanadate.
Authors: Paolillo, M. / Ferraro, G. / Gumerova, N.I. / Pisanu, F. / Garribba, E. / Rompel, A. / Merlino, A.
History
DepositionMay 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: 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)15,7326
Polymers14,3311
Non-polymers1,4015
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 78.600, 35.650
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-315-

HOH

21AAA-334-

HOH

31AAA-344-

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, 80 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.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O28V10 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1JFD / 2-[(4~{S})-1,1,6,6-tetrakis(oxidanyl)-3-oxidanylidene-2,5$l^{3},7-trioxa-1$l^{5},6$l^{4}-divanadabicyclo[3.2.0]heptan-4-yl]ethanoic acid / dioxovanadium(V) complex of malic acid


Mass: 317.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O10V2
#6: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
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: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→55.586 Å / Num. obs: 17932 / % possible obs: 88.9 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 27.4
Reflection shellResolution: 1.46→1.48 Å / Num. unique obs: 542 / CC1/2: 0.498

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→55.586 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.558 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3124 807 4.905 %
Rwork0.2388 15647 -
all0.242 --
obs-16454 82.389 %
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: 27.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.199 Å2
Refinement stepCycle: LAST / Resolution: 1.46→55.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 38 75 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141029
X-RAY DIFFRACTIONr_ext_dist_refined_d00.011
X-RAY DIFFRACTIONr_angle_refined_deg1.91.6971583
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5992352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12520.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6815191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2231514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021339
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_nbd_refined0.250.2291
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.2993
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2554
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.248
X-RAY DIFFRACTIONr_metal_ion_refined0.160.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.224
X-RAY DIFFRACTIONr_nbd_other0.190.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0630.21
X-RAY DIFFRACTIONr_mcbond_it2.3122.698550
X-RAY DIFFRACTIONr_mcbond_other2.2852.688549
X-RAY DIFFRACTIONr_mcangle_it3.284.04698
X-RAY DIFFRACTIONr_mcangle_other3.294.049699
X-RAY DIFFRACTIONr_scbond_it2.8353.123603
X-RAY DIFFRACTIONr_scbond_other2.5872.988560
X-RAY DIFFRACTIONr_scangle_it4.1894.552872
X-RAY DIFFRACTIONr_scangle_other4.0824.386818
X-RAY DIFFRACTIONr_lrange_it6.2732.5891380
X-RAY DIFFRACTIONr_lrange_other6.20532.1981364
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
1.46-1.4980.376300.3415220.34314450.7510.75438.20070.333
1.498-1.5390.322490.2897680.29114160.8480.83657.69770.267
1.539-1.5830.319530.2829750.28413640.8710.86375.36660.251
1.583-1.6320.297390.30110440.30113350.8550.83181.12360.265
1.632-1.6860.421500.32611000.3312900.7080.75989.14730.274
1.686-1.7450.375550.30710070.3112570.8020.8384.48690.258
1.745-1.8110.364580.32910990.33112150.7680.80595.22630.265
1.811-1.8840.444550.3139520.32111830.7660.82885.12260.256
1.884-1.9680.478330.2997760.30611160.810.84772.4910.249
1.968-2.0640.374670.2799090.28510700.8440.87491.2150.243
2.064-2.1760.354460.2719100.27510270.8470.89393.08670.248
2.176-2.3070.299380.2628320.2649820.8840.89688.59470.247
2.307-2.4660.34310.2558860.2589300.8430.89398.60210.252
2.466-2.6630.36450.2467450.2538550.8570.89592.39770.246
2.663-2.9170.296310.237460.2328030.8710.91396.76210.249
2.917-3.260.258380.216900.2127360.9130.94298.9130.242
3.26-3.7620.269260.2055100.2076470.9160.95782.84390.229
3.762-4.6030.214270.1684840.175640.9550.9790.60280.211
4.603-6.4870.287250.2224250.2264500.9430.9531000.277
6.487-55.5860.359110.2452660.2492830.9240.94497.87990.305

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