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- PDB-7zu6: Polyoxidovanadate interaction with proteins: crystal structure of... -

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Basic information

Entry
Database: PDB / ID: 7zu6
TitlePolyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to tetra-vanadate ion (structure 1)
ComponentsLysozyme
KeywordsHYDROLASE / protein / vanadium / metallodrug / polyoxidovanadate ions / interaction
Function / homology
Function and homology information


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 Gram-positive bacterium / defense response to bacterium ...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 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
CYCLO-TETRAMETAVANADATE / bis(oxidanyl)vanadium / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.183 Å
AuthorsTito, G. / Merlino, A. / Ferraro, G.
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
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 13, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0735
Polymers14,3311
Non-polymers7424
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-10 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.050, 77.050, 37.840
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-353-

HOH

21AAA-361-

HOH

31AAA-478-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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, lysozyme

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Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-V4O / CYCLO-TETRAMETAVANADATE


Mass: 395.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O12V4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VVB / bis(oxidanyl)vanadium


Mass: 84.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2V / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 37.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M sodium formate 0.1 M hepes buffer 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: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.18→38.52 Å / Num. obs: 37733 / % possible obs: 99.9 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.1
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1844 / CC1/2: 0.847 / % possible all: 100

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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: 1.183→38.52 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.73 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1961 1755 4.83 %
Rwork0.1707 34580 -
all0.172 --
obs-36335 96.285 %
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: 18.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å20 Å20 Å2
2---0.004 Å20 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.183→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 35 178 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141041
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.6641568
X-RAY DIFFRACTIONr_angle_other_deg1.6441.5972384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52620.44168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32115187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2771513
X-RAY DIFFRACTIONr_chiral_restr0.1130.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
X-RAY DIFFRACTIONr_nbd_refined0.2390.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21001
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2572
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.290
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.221
X-RAY DIFFRACTIONr_nbd_other0.2060.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0540.21
X-RAY DIFFRACTIONr_mcbond_it1.4351.532559
X-RAY DIFFRACTIONr_mcbond_other1.4231.531559
X-RAY DIFFRACTIONr_mcangle_it2.1342.309714
X-RAY DIFFRACTIONr_mcangle_other2.1412.313715
X-RAY DIFFRACTIONr_scbond_it2.7841.935588
X-RAY DIFFRACTIONr_scbond_other2.7231.904568
X-RAY DIFFRACTIONr_scangle_it4.2262.788854
X-RAY DIFFRACTIONr_scangle_other4.1662.738830
X-RAY DIFFRACTIONr_lrange_it5.99120.1351413
X-RAY DIFFRACTIONr_lrange_other5.79219.291371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.183-1.2140.284860.2721806X-RAY DIFFRACTION69.0511
1.214-1.2470.291990.2632098X-RAY DIFFRACTION82.937
1.247-1.2830.2521280.242410X-RAY DIFFRACTION97.3159
1.322-1.3660.2671240.2192327X-RAY DIFFRACTION100
1.366-1.4140.2521080.2072269X-RAY DIFFRACTION100
1.414-1.4670.2171050.1962180X-RAY DIFFRACTION100
1.467-1.5270.1991240.1842105X-RAY DIFFRACTION99.9104
1.527-1.5950.2151130.1712019X-RAY DIFFRACTION100
1.595-1.6720.1871020.1661931X-RAY DIFFRACTION100
1.672-1.7620.177910.1731858X-RAY DIFFRACTION100
1.762-1.8690.184900.1671761X-RAY DIFFRACTION99.946
1.998-2.1570.168760.1541540X-RAY DIFFRACTION99.9382
2.157-2.3630.167680.1471447X-RAY DIFFRACTION99.8682
2.363-2.640.165560.1471308X-RAY DIFFRACTION100
2.64-3.0460.231670.1641165X-RAY DIFFRACTION100
3.046-3.7250.183440.1471011X-RAY DIFFRACTION100
3.725-5.2440.164430.142793X-RAY DIFFRACTION99.7613

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