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- PDB-9ex1: X-ray structure of a polyoxidovanadate/lysozyme adduct obtained w... -

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Basic information

Entry
Database: PDB / ID: 9ex1
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 B)
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / vanadium / acetoacetonate / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.785 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)15,6593
Polymers14,3311
Non-polymers1,3282
Water72140
1
A: Lysozyme C
hetero molecules

A: Lysozyme C
hetero molecules


  • defined by author
  • 31.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)31,3176
Polymers28,6622
Non-polymers2,6554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Unit cell
Length a, b, c (Å)77.800, 77.800, 35.350
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-

A1H8D

21A-202-

A1H8D

31A-202-

A1H8D

41A-312-

HOH

51A-320-

HOH

61A-329-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-A1H8D / Polyoxidovanadate complex


Mass: 1292.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O33V15 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 1.87 Å3/Da / Density % sol: 34.09 %
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: 1.78→38.93 Å / Num. obs: 10434 / % possible obs: 96.3 % / Redundancy: 22.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.017 / Rrim(I) all: 0.079 / Net I/σ(I): 19
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 24 % / Rmerge(I) obs: 2.151 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12610 / CC1/2: 0.923 / Rpim(I) all: 0.445 / Rrim(I) all: 2.197 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.785→38.93 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.235 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.257 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3 430 4.964 %
Rwork0.2482 8232 -
all0.251 --
obs-8662 80.293 %
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: 37.112 Å2
Baniso -1Baniso -2Baniso -3
1--1.017 Å20 Å2-0 Å2
2---1.017 Å20 Å2
3---2.035 Å2
Refinement stepCycle: LAST / Resolution: 1.785→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 28 40 1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0111082
X-RAY DIFFRACTIONr_bond_other_d0.0010.016899
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.5981481
X-RAY DIFFRACTIONr_angle_other_deg0.4621.5622098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.465132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.498511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07410171
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.951052
X-RAY DIFFRACTIONr_chiral_restr0.0650.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_nbd_refined0.2280.2261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.2922
X-RAY DIFFRACTIONr_nbtor_refined0.180.2539
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.225
X-RAY DIFFRACTIONr_nbd_other0.160.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.212
X-RAY DIFFRACTIONr_mcbond_it3.2013.825525
X-RAY DIFFRACTIONr_mcbond_other3.1993.823525
X-RAY DIFFRACTIONr_mcangle_it4.5715.72658
X-RAY DIFFRACTIONr_mcangle_other4.5785.735659
X-RAY DIFFRACTIONr_scbond_it3.2264.091557
X-RAY DIFFRACTIONr_scbond_other3.2344.132525
X-RAY DIFFRACTIONr_scangle_it4.6816.035817
X-RAY DIFFRACTIONr_scangle_other4.7496.085769
X-RAY DIFFRACTIONr_lrange_it8.27660.6031312
X-RAY DIFFRACTIONr_lrange_other8.28359.3171308
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
1.785-1.8310.281160.1724040.1777660.9520.97854.83030.137
1.831-1.8810.389150.2914150.2957570.9050.93856.80320.248
1.881-1.9360.327230.3154450.3167380.9070.9263.41460.263
1.936-1.9950.449220.334730.3367290.810.90867.90120.28
1.995-2.060.402310.3384690.3426900.8530.91272.46380.286
2.06-2.1330.355320.3094870.3126670.9040.9377.81110.257
2.133-2.2130.386190.2865150.296650.9090.9480.30080.255
2.213-2.3030.38330.2934980.2986260.9150.94284.82430.265
2.303-2.4050.266320.2814680.285970.9490.94483.75210.259
2.405-2.5220.548180.2684950.2765950.8680.94886.21850.262
2.522-2.6570.43270.2594750.2685440.9230.95492.27940.247
2.657-2.8180.281280.2754700.2755290.9280.94694.13990.283
2.818-3.0110.233230.2664360.2645040.9650.95391.07140.27
3.011-3.2510.356190.2544190.264720.930.95292.79660.267
3.251-3.5590.253180.2413940.2414380.940.95494.06390.258
3.559-3.9750.308190.2083540.2123880.9540.97196.1340.246
3.975-4.5820.202190.1913330.1913620.9840.97697.23760.238
4.582-5.5920.218170.212870.213040.9590.9731000.26
5.592-7.8280.267100.2282420.232520.9550.9561000.281
7.828-38.930.38590.271530.2751620.9310.9421000.297

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