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- PDB-5ob8: X-ray structure of the adduct formed upon reaction of lysozyme wi... -

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Basic information

Entry
Database: PDB / ID: 5ob8
TitleX-ray structure of the adduct formed upon reaction of lysozyme with the compound fac-[RuII(CO)3Cl2(N3-MIM), MIM=methyl-imidazole (crystals grown using NaCl)
ComponentsLysozyme C
KeywordsHYDROLASE / protein-metallodrug interaction / CO releasing molecules
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-9QB / ACETATE ION / Chem-RU2 / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPontillo, N. / Ferraro, G. / Merlino, A.
CitationJournal: Dalton Trans / Year: 2017
Title: Ru-Based CO releasing molecules with azole ligands: interaction with proteins and the CO release mechanism disclosed by X-ray crystallography.
Authors: Pontillo, N. / Ferraro, G. / Messori, L. / Tamasi, G. / Merlino, A.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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)15,0198
Polymers14,3311
Non-polymers6887
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-31 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.573, 78.573, 36.664
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-342-

HOH

21A-348-

HOH

31A-433-

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, 143 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-9QB / chloranyl-bis(oxidaniumyl)-tris(oxidaniumylidynemethyl)ruthenium


Mass: 256.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4ClO5Ru
#6: Chemical ChemComp-RU2 / pentakis(oxidaniumyl)-(oxidaniumylidynemethyl)ruthenium


Mass: 219.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH10O6Ru
#7: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.1M NaCl, 0.1 M sodium acetate pH 4.0

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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: Apr 7, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→55.56 Å / Num. obs: 9488 / % possible obs: 92.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 36.8
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.85→55.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.78 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 457 4.8 %RANDOM
Rwork0.15955 ---
obs0.163 8981 92.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.85→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 26 136 1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021086
X-RAY DIFFRACTIONr_bond_other_d0.0020.02957
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9521476
X-RAY DIFFRACTIONr_angle_other_deg1.10732212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27123.01953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36215179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1791512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021238
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02246
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_it2.8123.1535
X-RAY DIFFRACTIONr_mcbond_other2.7653.087532
X-RAY DIFFRACTIONr_mcangle_it3.5374.624669
X-RAY DIFFRACTIONr_mcangle_other3.5354.629670
X-RAY DIFFRACTIONr_scbond_it3.5733.462551
X-RAY DIFFRACTIONr_scbond_other3.4453.439539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0735.015785
X-RAY DIFFRACTIONr_long_range_B_refined6.77437.7671343
X-RAY DIFFRACTIONr_long_range_B_other6.77637.7811344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 31 -
Rwork0.256 577 -
obs--85.03 %

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