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- PDB-4z3m: X-ray structure of the adduct formed in the reaction between lyso... -

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Basic information

Entry
Database: PDB / ID: 4z3m
TitleX-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) Complex with S,O Bidentate Ligands (9b)
ComponentsLysozyme C
KeywordsHYDROLASE / Pt compounds / anticancer agents / lysozyme complexes
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
Chem-4KV / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMerlino, A.
CitationJournal: Inorg.Chem. / Year: 2015
Title: Platinum(II) Complexes with O,S Bidentate Ligands: Biophysical Characterization, Antiproliferative Activity, and Crystallographic Evidence of Protein Binding.
Authors: Mugge, C. / Marzo, T. / Massai, L. / Hildebrandt, J. / Ferraro, G. / Rivera-Fuentes, P. / Metzler-Nolte, N. / Merlino, A. / Messori, L. / Weigand, W.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,39310
Polymers14,3311
Non-polymers1,0619
Water1,802100
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint15 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.261, 78.261, 36.878
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-362-

HOH

21A-371-

HOH

31A-397-

HOH

41A-398-

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, 109 molecules

#2: Chemical ChemComp-4KV / 3-[2-chloranyl-2-[dimethyl(oxidanyl)-{4}-sulfanyl]-4-ethylsulfanyl-1-oxa-3{3}-thia-2{4}-platinacyclohexa-3,5-dien-6-yl]phenol


Mass: 549.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18ClO3PtS3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% ethylene glycol, 0.1 M sodium acetate pH 4.5, 0.6 M sodium nitrate
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: No cryoprotectant was used
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 17, 2014
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→55.34 Å / Num. all: 43330 / Num. obs: 6498 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 11
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4j4t

4j4t


Resolution: 2.15→55.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.549 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23267 303 4.7 %RANDOM
Rwork0.16032 ---
obs0.16354 6177 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.15→55.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 52 100 1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191082
X-RAY DIFFRACTIONr_bond_other_d0.0020.02979
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9411456
X-RAY DIFFRACTIONr_angle_other_deg0.99532225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17122.74551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83815169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.221512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
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_it1.9422.52520
X-RAY DIFFRACTIONr_mcbond_other1.9432.517519
X-RAY DIFFRACTIONr_mcangle_it2.9363.774650
X-RAY DIFFRACTIONr_mcangle_other2.9343.777651
X-RAY DIFFRACTIONr_scbond_it2.9242.946559
X-RAY DIFFRACTIONr_scbond_other2.9182.946559
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6044.241805
X-RAY DIFFRACTIONr_long_range_B_refined6.65621.671321
X-RAY DIFFRACTIONr_long_range_B_other6.65521.6861322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 19 -
Rwork0.193 447 -
obs--99.36 %

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