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- PDB-5v4i: Osmium(II)(cymene)(chlorido)2-lysozyme adduct with one binding site -

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Basic information

Entry
Database: PDB / ID: 5v4i
TitleOsmium(II)(cymene)(chlorido)2-lysozyme adduct with one binding site
ComponentsLysozyme C
KeywordsHYDROLASE / Metal-based / anticancer / osmium / lysozyme
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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-8WV / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSullivan, M.P. / Hartinger, C.G. / Goldstone, D.C.
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: The metalation of hen egg white lysozyme impacts protein stability as shown by ion mobility mass spectrometry, differential scanning calorimetry, and X-ray crystallography.
Authors: Sullivan, M.P. / Groessl, M. / Meier, S.M. / Kingston, R.L. / Goldstone, D.C. / Hartinger, C.G.
History
DepositionMar 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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)14,7453
Polymers14,3311
Non-polymers4142
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.594, 80.594, 36.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-8WV / dichloro[(1,2,3,4,5,6-eta)-3-methyl-6-(propan-2-yl)benzene-1,2,4,5-tetrayl]osmium


Mass: 391.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10Cl2Os
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mg/mL hen egg white lysozyme, 0.8 M NaCl, 0.1 M sodium acetate pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 20117 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.05 / Rrim(I) all: 0.152 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.537.60.8079670.7750.2920.861100
8.22-36.046.90.0830.9940.0310.08999.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.54 Å36.04 Å
Translation5.54 Å36.04 Å

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Processing

Software
NameVersionClassification
XDSOct 15, 2015data reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
Coot0.8.3model building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NHI

4nhi


Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.787 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 956 4.8 %RANDOM
Rwork0.2299 ---
obs0.2322 19120 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.62 Å2 / Biso mean: 19.123 Å2 / Biso min: 9.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 71 1086
Biso mean--28.02 26.57 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191086
X-RAY DIFFRACTIONr_bond_other_d0.0020.021008
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9451510
X-RAY DIFFRACTIONr_angle_other_deg0.99632299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48622.40754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0291514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02291
X-RAY DIFFRACTIONr_rigid_bond_restr1.20632093
X-RAY DIFFRACTIONr_sphericity_free27.593528
X-RAY DIFFRACTIONr_sphericity_bonded8.11452103
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 90 -
Rwork0.518 1371 -
all-1461 -
obs--100 %

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