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- PDB-6zs8: X-ray structure of the adduct formed upon treating lysozyme with ... -

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Basic information

Entry
Database: PDB / ID: 6zs8
TitleX-ray structure of the adduct formed upon treating lysozyme with an aged solution of arsenoplatin-1
ComponentsLysozyme
KeywordsHYDROLASE / platinum / aresenic / bimetallin / protein binding / aggregation
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
arsenoplatin-1 / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsFerraro, G. / Merlino, A.
CitationJournal: Dalton Trans / Year: 2021
Title: The first step of arsenoplatin-1 aggregation in solution unveiled by solving the crystal structure of its protein adduct.
Authors: Ferraro, G. / Cirri, D. / Marzo, T. / Pratesi, A. / Messori, L. / Merlino, A.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,66915
Polymers14,3311
Non-polymers3,33814
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-1 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.703, 78.703, 34.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 , 6 types, 74 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-A6R / arsenoplatin-1


Mass: 418.117 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8AsN2O4Pt / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.86 Å3/Da / Density % sol: 33.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→55.65 Å / Num. obs: 6242 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.639 / Num. unique obs: 301 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J1A

4j1a


Resolution: 2.153→25.939 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.121 / SU ML: 0.176 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2389 289 4.646 %
Rwork0.1847 5932 -
all0.187 --
obs-6221 99.632 %
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: 32.612 Å2
Baniso -1Baniso -2Baniso -3
1--0.658 Å20 Å20 Å2
2---0.658 Å20 Å2
3---1.315 Å2
Refinement stepCycle: LAST / Resolution: 2.153→25.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 76 60 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131105
X-RAY DIFFRACTIONr_bond_other_d0.0010.018928
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0630.017
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.7311512
X-RAY DIFFRACTIONr_angle_other_deg1.3221.5882140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9175130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61320.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93915170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0721511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0221321
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_nbd_refined0.2340.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.2908
X-RAY DIFFRACTIONr_nbtor_refined0.160.2510
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.251
X-RAY DIFFRACTIONr_metal_ion_refined0.270.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.228
X-RAY DIFFRACTIONr_nbd_other0.2770.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.22
X-RAY DIFFRACTIONr_mcbond_it2.3013.39520
X-RAY DIFFRACTIONr_mcbond_other2.3023.387519
X-RAY DIFFRACTIONr_mcangle_it3.6745.074650
X-RAY DIFFRACTIONr_mcangle_other3.6725.077651
X-RAY DIFFRACTIONr_scbond_it2.7243.701585
X-RAY DIFFRACTIONr_scbond_other2.7223.702586
X-RAY DIFFRACTIONr_scangle_it4.2495.449862
X-RAY DIFFRACTIONr_scangle_other4.2475.45863
X-RAY DIFFRACTIONr_lrange_it7.11438.7591388
X-RAY DIFFRACTIONr_lrange_other7.11238.7731389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.153-2.2090.406310.212417X-RAY DIFFRACTION100
2.209-2.2690.377170.195420X-RAY DIFFRACTION100
2.269-2.3350.375270.221398X-RAY DIFFRACTION100
2.335-2.4070.369150.21390X-RAY DIFFRACTION100
2.407-2.4850.22190.2398X-RAY DIFFRACTION100
2.485-2.5720.306230.187352X-RAY DIFFRACTION100
2.572-2.6690.392150.18376X-RAY DIFFRACTION100
2.669-2.7780.201180.173341X-RAY DIFFRACTION99.7222
2.778-2.9010.344160.198339X-RAY DIFFRACTION100
2.901-3.0420.22130.172323X-RAY DIFFRACTION100
3.042-3.2060.194160.178304X-RAY DIFFRACTION100
3.206-3.40.219120.163292X-RAY DIFFRACTION100
3.4-3.6340.212180.166274X-RAY DIFFRACTION100
3.634-3.9240.27190.17262X-RAY DIFFRACTION99.2674
3.924-4.2960.1390.149247X-RAY DIFFRACTION100

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