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- PDB-4zee: X-ray structure of the bis-platinum lysozyme adduct formed in the... -

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Basic information

Entry
Database: PDB / ID: 4zee
TitleX-ray structure of the bis-platinum lysozyme adduct formed in the reaction between the protein and the two drugs Cisplatin and Oxaliplatin (preparation 2)
ComponentsLysozyme C
KeywordsHYDROLASE / ciapltin / oxaliplatin / platin based drugs / cancer
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
CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) / Cisplatin / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMerlino, A.
CitationJournal: Dalton Trans / Year: 2015
Title: Oxaliplatin vs. cisplatin: competition experiments on their binding to lysozyme.
Authors: Marasco, D. / Messori, L. / Marzo, T. / Merlino, A.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 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 1.3Nov 13, 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)15,62314
Polymers14,3311
Non-polymers1,29113
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint5 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.377, 77.377, 37.600
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-409-

NO3

21A-409-

NO3

31A-555-

HOH

41A-636-

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, 149 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1PT / CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) / OXALIPLATIN


Mass: 309.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2Pt / Comment: medication, antineoplastic*YM
#5: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.96 Å3/Da / Density % sol: 37.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: Best crystals grow within 2-10 days from the following conditions: 0.6 M NaNO3, 0.1 M sodium acetate pH 4.4 and 20 % ethylene glycol.
PH range: 4.4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: no cryoprotectant
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→54.71 Å / Num. obs: 8452 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.611 / % possible all: 83.2

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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: 4J1A

4j1a


Resolution: 1.95→54.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.418 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22986 403 4.8 %RANDOM
Rwork0.15877 ---
obs0.16223 8023 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.95→54.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 56 136 1193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191087
X-RAY DIFFRACTIONr_bond_other_d0.0020.02977
X-RAY DIFFRACTIONr_angle_refined_deg4.9311.9431461
X-RAY DIFFRACTIONr_angle_other_deg1.4232224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53423.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27915168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7821511
X-RAY DIFFRACTIONr_chiral_restr0.1170.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021289
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02280
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_it2.0132.408525
X-RAY DIFFRACTIONr_mcbond_other1.9812.403524
X-RAY DIFFRACTIONr_mcangle_it2.8153.597658
X-RAY DIFFRACTIONr_mcangle_other2.823.6659
X-RAY DIFFRACTIONr_scbond_it3.7172.853559
X-RAY DIFFRACTIONr_scbond_other3.7152.858560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0934.12800
X-RAY DIFFRACTIONr_long_range_B_refined7.86821.5831378
X-RAY DIFFRACTIONr_long_range_B_other7.65620.8081321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 34 -
Rwork0.234 502 -
obs--84.41 %

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