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- PDB-5e9r: X-ray structure of the complex between lysozyme and the compound ... -

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Basic information

Entry
Database: PDB / ID: 5e9r
TitleX-ray structure of the complex between lysozyme and the compound fac, cis-[RuII(CO)3Cl2(N3-MBI), MBI=N-methyl-benzimidazole
ComponentsLysozyme C
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL)
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-5LN / CARBON MONOXIDE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsMerlino, A.
CitationJournal: To Be Published
Title: {Ru(CO)x}-core Complexes with N-Methylbenzimidazole (MBI) and 5,6-Dimethylbenzimidazole (DMBI) as Possible Metal Based Drugs and CO Release Materials. Synthesis, X-ray Structure and Evaluation ...Title: {Ru(CO)x}-core Complexes with N-Methylbenzimidazole (MBI) and 5,6-Dimethylbenzimidazole (DMBI) as Possible Metal Based Drugs and CO Release Materials. Synthesis, X-ray Structure and Evaluation of Cytotoxic Activity against Human Cancer Cells
Authors: Merlino, A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,7217
Polymers14,3311
Non-polymers3906
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-37 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.500, 78.500, 36.309
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-449-

HOH

21A-459-

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, 165 molecules

#2: Chemical ChemComp-5LN / chloranyl-bis(hydroxymethyl)-bis(oxidanyl)ruthenium / Ru(CO)2Cl(OH2)2


Mass: 232.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H8ClO4Ru
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Hen egg white lysozyme was incubated for 2 h in the presence of Ru-MBI in 1:10 protein to metal compound ratio. The adduct was then crystallized by using the hanging drop vapour diffusion ...Details: Hen egg white lysozyme was incubated for 2 h in the presence of Ru-MBI in 1:10 protein to metal compound ratio. The adduct was then crystallized by using the hanging drop vapour diffusion method. Drops of 1 microliter were prepared at room temperature mixing 0.5 microliter of adduct at concentration 15 mg/mL with an equal amount of a reservoir constituted by 1.1 M NaCl, 0.1 M acetate buffer, pH 4.0. Crystals of the adduct grow within 24-48 hours.
PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→55.5 Å / Num. obs: 5740 / % possible obs: 99.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.25→55.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.658 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23734 261 4.6 %RANDOM
Rwork0.15228 ---
obs0.15626 5452 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.896 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å20 Å2
2---0.92 Å20 Å2
3---1.84 Å2
Refinement stepCycle: 1 / Resolution: 2.25→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 159 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021050
X-RAY DIFFRACTIONr_bond_other_d0.0010.02952
X-RAY DIFFRACTIONr_angle_refined_deg2.7811.9271428
X-RAY DIFFRACTIONr_angle_other_deg0.86432169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11723.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36115168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.331511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021240
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_it2.0953.198525
X-RAY DIFFRACTIONr_mcbond_other2.0493.187524
X-RAY DIFFRACTIONr_mcangle_it3.1134.784658
X-RAY DIFFRACTIONr_mcangle_other3.1384.795659
X-RAY DIFFRACTIONr_scbond_it3.0473.583525
X-RAY DIFFRACTIONr_scbond_other2.9983.571517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9185.214758
X-RAY DIFFRACTIONr_long_range_B_refined7.25927.2191402
X-RAY DIFFRACTIONr_long_range_B_other7.13126.7691351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 19 -
Rwork0.15 396 -
obs--100 %

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