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- PDB-9ex2: X-ray structure of a polyoxidovanadate/lysozyme adduct obtained w... -

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Basic information

Entry
Database: PDB / ID: 9ex2
TitleX-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure C)
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / vanadium / POV / cluster / mixed valence
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
: / VANADATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.172 Å
AuthorsTito, G. / Merlino, A. / Ferraro, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2022JMFC3X Italy
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Non-Covalent and Covalent Binding of New Mixed-Valence Cage-like Polyoxidovanadate Clusters to Lysozyme.
Authors: Tito, G. / Ferraro, G. / Pisanu, F. / Garribba, E. / Merlino, A.
History
DepositionApr 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,42511
Polymers14,3311
Non-polymers3,09410
Water3,243180
1
A: Lysozyme C
hetero molecules

A: Lysozyme C
hetero molecules


  • defined by author
  • 34.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)34,85022
Polymers28,6622
Non-polymers6,18820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)78.330, 78.330, 37.050
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-202-

VO4

21A-202-

VO4

31A-202-

VO4

41A-203-

A1H8D

51A-203-

A1H8D

61A-203-

A1H8D

71A-332-

HOH

81A-351-

HOH

91A-370-

HOH

101A-469-

HOH

111A-480-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 , 5 types, 190 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1H8D / Polyoxidovanadate complex


Mass: 1292.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O33V15 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.1 M NaCl, 0.1 M sodium acetate at 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 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→55.39 Å / Num. obs: 41982 / % possible obs: 99.1 % / Redundancy: 23.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Net I/σ(I): 15.3
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2069 / CC1/2: 0.796 / Rsym value: 1.204 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.172→55.388 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.385 / SU ML: 0.029 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1891 1923 4.949 %
Rwork0.1557 36936 -
all0.157 --
obs-38859 99.016 %
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: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.092 Å2-0 Å20 Å2
2--0.092 Å2-0 Å2
3----0.184 Å2
Refinement stepCycle: LAST / Resolution: 1.172→55.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 94 180 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0121232
X-RAY DIFFRACTIONr_bond_other_d0.0030.016967
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.5871731
X-RAY DIFFRACTIONr_angle_other_deg0.6441.5672262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.833514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4510190
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.4861056
X-RAY DIFFRACTIONr_chiral_restr0.1020.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021368
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_nbd_refined0.2790.2316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2931
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2547
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2060.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.240
X-RAY DIFFRACTIONr_nbd_other0.2380.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.248
X-RAY DIFFRACTIONr_mcbond_it1.6121.518555
X-RAY DIFFRACTIONr_mcbond_other1.61.518555
X-RAY DIFFRACTIONr_mcangle_it1.9092.291706
X-RAY DIFFRACTIONr_mcangle_other1.9092.293707
X-RAY DIFFRACTIONr_scbond_it3.2521.911677
X-RAY DIFFRACTIONr_scbond_other2.8771.843562
X-RAY DIFFRACTIONr_scangle_it3.6682.7871001
X-RAY DIFFRACTIONr_scangle_other3.2632.659818
X-RAY DIFFRACTIONr_lrange_it3.73133.3151493
X-RAY DIFFRACTIONr_lrange_other3.49330.1551448
X-RAY DIFFRACTIONr_rigid_bond_restr5.10432199
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
1.172-1.2020.2541590.2126930.21328520.970.9781000.193
1.202-1.2350.4571370.37624360.3827770.8730.91192.65390.349
1.235-1.2710.2381250.20825700.20926950.9620.9771000.186
1.271-1.310.2931200.30323360.30326280.9450.9493.45510.275
1.31-1.3530.1981170.17624360.17725530.9760.9831000.16
1.353-1.4010.181200.14623750.14824950.980.9881000.134
1.401-1.4540.2171010.13822680.14123690.9740.9891000.129
1.454-1.5130.1611290.12221810.12423160.9850.9999.74090.119
1.513-1.580.1671030.11321060.11622090.9820.9911000.115
1.58-1.6570.1711080.10820160.11121240.9810.9921000.116
1.657-1.7470.154890.11719390.11920280.9830.9911000.129
1.747-1.8520.172990.12218290.12419280.9820.991000.14
1.852-1.980.189830.16917220.1718050.9760.9811000.184
1.98-2.1390.17860.1316010.13216870.9810.991000.157
2.139-2.3420.186820.15415010.15515830.9750.9841000.181
2.342-2.6180.173720.13813500.13914220.980.9871000.174
2.618-3.0220.189690.14412000.14612690.9760.9861000.187
3.022-3.6990.186580.14810440.1511020.9740.9861000.192
3.699-5.2190.161430.1448200.1458630.9880.9881000.199
5.219-55.3880.233220.2635030.2625290.9510.9599.24390.385

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