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- PDB-5ilf: The X-ray structure of the adduct formed in the reaction between ... -

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Basic information

Entry
Database: PDB / ID: 5ilf
TitleThe X-ray structure of the adduct formed in the reaction between hen egg white lysozyme and compound 4, a platin(II) compound containing a O, S bidentate ligand
ComponentsLysozyme C
KeywordsHYDROLASE / metallodrug / protein platination
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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Dalton Trans / Year: 2016
Title: Platinum(ii) O,S complexes as potential metallodrugs against Cisplatin resistance.
Authors: Hildebrandt, J. / Hafner, N. / Gorls, H. / Kritsch, D. / Ferraro, G. / Durst, M. / Runnebaum, I.B. / Merlino, A. / Weigand, W.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 13, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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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)14,8289
Polymers14,3311
Non-polymers4978
Water2,342130
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-64 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.983, 77.983, 37.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-347-

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 , 6 types, 138 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystals of hen egg white lysozyme (HEWL)-Pt compound adducts appeared in solutions consisting of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4. Single crystals suitable for X-ray experiments were ...Details: Crystals of hen egg white lysozyme (HEWL)-Pt compound adducts appeared in solutions consisting of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4. Single crystals suitable for X-ray experiments were grown by the hanging drop vapor-diffusion method using a 1:1 ratio of reservoir solution and protein adducts solution with a protein concentration of about 15 mg / ml.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→55.14 Å / Num. obs: 10170 / % possible obs: 98.6 % / Redundancy: 5.1 % / Net I/σ(I): 9.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 5.1 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J1A

4j1a


Resolution: 1.85→55.14 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.156 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 478 4.7 %RANDOM
Rwork0.167 ---
obs0.17 9669 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 130 1145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191071
X-RAY DIFFRACTIONr_bond_other_d0.0020.02983
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9131455
X-RAY DIFFRACTIONr_angle_other_deg1.13232238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5745136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30722.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6551512
X-RAY DIFFRACTIONr_chiral_restr0.1350.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021282
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9222.121536
X-RAY DIFFRACTIONr_mcbond_other1.8962.111534
X-RAY DIFFRACTIONr_mcangle_it2.5433.164674
X-RAY DIFFRACTIONr_mcangle_other2.5473.169675
X-RAY DIFFRACTIONr_scbond_it3.0692.488534
X-RAY DIFFRACTIONr_scbond_other3.0672.492535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6153.601783
X-RAY DIFFRACTIONr_long_range_B_refined6.38618.3691371
X-RAY DIFFRACTIONr_long_range_B_other6.38418.3741372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 32 -
Rwork0.185 645 -
obs--92.11 %

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