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

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Basic information

Entry
Database: PDB / ID: 9rbt
TitleX-ray structure of decavanadate/lysozyme adduct obtained when the protein is treated with Cs2[V(V)2O4(mal)2]2H2O (structure B)
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
: / ACETATE ION / DECAVANADATE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)15,7837
Polymers14,3311
Non-polymers1,4526
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-24 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.010, 80.010, 36.270
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-331-

HOH

21AAA-388-

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, 115 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O28V10 / Feature type: SUBJECT OF INVESTIGATION
#6: 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 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.03 Å3/Da / Density % sol: 39.26 %
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: Oct 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→40.01 Å / Num. obs: 35010 / % possible obs: 89.1 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 1.18→1.2 Å / Num. unique obs: 1939 / CC1/2: 0.371

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→40.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.37 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2347 1341 4.7 %
Rwork0.1914 27190 -
all0.193 --
obs-28531 72.622 %
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: 25.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.564 Å20 Å20 Å2
2---0.564 Å20 Å2
3---1.129 Å2
Refinement stepCycle: LAST / Resolution: 1.18→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 45 109 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121104
X-RAY DIFFRACTIONr_bond_other_d0.0020.014974
X-RAY DIFFRACTIONr_angle_refined_deg2.4141.6951514
X-RAY DIFFRACTIONr_angle_other_deg1.6421.5932221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24520.80662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27115172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2071511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02288
X-RAY DIFFRACTIONr_nbd_refined0.2490.2275
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.2977
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2533
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.258
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.217
X-RAY DIFFRACTIONr_nbd_other0.1740.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0440.21
X-RAY DIFFRACTIONr_mcbond_it3.4992.338532
X-RAY DIFFRACTIONr_mcbond_other3.482.325529
X-RAY DIFFRACTIONr_mcangle_it4.1393.503666
X-RAY DIFFRACTIONr_mcangle_other4.143.515667
X-RAY DIFFRACTIONr_scbond_it5.8112.853571
X-RAY DIFFRACTIONr_scbond_other5.0032.772530
X-RAY DIFFRACTIONr_scangle_it7.2364.11834
X-RAY DIFFRACTIONr_scangle_other6.1074.002777
X-RAY DIFFRACTIONr_lrange_it6.12428.8741316
X-RAY DIFFRACTIONr_lrange_other5.48928.1941291
X-RAY DIFFRACTIONr_rigid_bond_restr5.26432077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.2110.278210.271424X-RAY DIFFRACTION15.5758
1.211-1.2440.359300.282680X-RAY DIFFRACTION25.6133
1.244-1.280.325600.2511223X-RAY DIFFRACTION47.5009
1.28-1.3190.305600.231353X-RAY DIFFRACTION53.5633
1.319-1.3620.272810.2151720X-RAY DIFFRACTION70.4617
1.362-1.410.271850.2071662X-RAY DIFFRACTION70.8435
1.41-1.4630.2681010.2361984X-RAY DIFFRACTION86.407
1.463-1.5230.319940.2411724X-RAY DIFFRACTION79.0779
1.523-1.5910.2521000.2112093X-RAY DIFFRACTION99.0963
1.591-1.6680.279990.1952004X-RAY DIFFRACTION98.7324
1.668-1.7580.296840.1951686X-RAY DIFFRACTION87.5804
1.758-1.8650.232870.1991775X-RAY DIFFRACTION96.5267
1.865-1.9930.203540.1991268X-RAY DIFFRACTION73.1195
1.993-2.1520.214700.1851479X-RAY DIFFRACTION91.0641
2.152-2.3570.204750.1771366X-RAY DIFFRACTION91.9592
2.357-2.6340.246600.1961350X-RAY DIFFRACTION98.5325
2.634-3.0390.261640.1861133X-RAY DIFFRACTION93.7353
3.039-3.7170.24490.181959X-RAY DIFFRACTION92.1389
3.717-5.2340.18390.165803X-RAY DIFFRACTION96.3387
5.234-40.010.22280.214504X-RAY DIFFRACTION100

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