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- PDB-6tvl: Hen Egg White Lysozyme in complex with a "half sandwich"-type Ru(... -

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Basic information

Entry
Database: PDB / ID: 6tvl
TitleHen Egg White Lysozyme in complex with a "half sandwich"-type Ru(II) coordination compound
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / Ru(II) complex / anticancer compound
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-NYN / trifluoromethanesulfonic acid / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.395 Å
AuthorsChiniadis, L. / Giastas, P. / Bratsos, I. / Papakyriakou, A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: High-resolution crystal structures of a "half sandwich"-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K.
Authors: Chiniadis, L. / Bratsos, I. / Bethanis, K. / Karpusas, M. / Giastas, P. / Papakyriakou, A.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8775
Polymers14,3311
Non-polymers5464
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.270, 79.270, 35.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-355-

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, 120 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NYN / chlorido(1,2-diaminoethane-k2N,N')(1,4,7-trithiacyclononane-k3S,S',S'')ruthenium(II) trifluoromethanesulfonate


Mass: 337.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2RuS3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TFS / trifluoromethanesulfonic acid / Triflic acid


Mass: 150.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHF3O3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 37.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: NaCl 0.7-1.5 M, 0.1 M Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.395→35.451 Å / Num. obs: 23013 / % possible obs: 98.45 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02074 / Rpim(I) all: 0.02074 / Rrim(I) all: 0.02933 / Net I/σ(I): 15
Reflection shellResolution: 1.395→1.445 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1811 / Mean I/σ(I) obs: 3.75 / Num. unique obs: 2192 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.1811 / Rrim(I) all: 0.2561 / % possible all: 95.35

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.395→35.451 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.34
RfactorNum. reflection% reflection
Rfree0.2427 1132 4.92 %
Rwork0.221 --
obs0.2221 23013 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.79 Å2 / Biso mean: 29.0147 Å2 / Biso min: 14.07 Å2
Refinement stepCycle: final / Resolution: 1.395→35.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 24 116 1141
Biso mean--37.56 35.64 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.395-1.45850.31861350.308261296
1.4585-1.53540.34161280.2932266597
1.5354-1.63160.30671460.266269299
1.6316-1.75760.27371370.2535273199
1.7576-1.93450.29411510.2391272399
1.9345-2.21430.23971350.2237274099
2.2143-2.78970.20751500.2165278799
2.7897-35.4510.22961500.1995293199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42410.19440.41220.26460.26160.78780.20110.3629-0.2783-0.0845-0.10130.29630.1711-0.2523-0.04530.32290.0375-0.4790.2594-0.23930.468872.899516.415126.6711
21.2453-0.30260.64453.94860.08511.5280.161-0.0272-0.2396-0.1115-0.00940.42180.2035-0.2528-0.18720.118-0.013-0.04540.2358-0.02410.4667.828723.835337.2265
31.3266-0.55480.30250.647-0.03420.4020.13130.197-0.3515-0.3345-0.21620.3174-0.1437-0.0333-0.00390.24040.0377-0.10370.1712-0.03670.210577.685824.901630.2442
42.1784-0.73441.15021.09290.39462.29050.0382-0.1042-0.2041-0.2340.04340.3027-0.18240.0809-0.05250.18370.0258-0.05680.1806-0.02780.186989.610618.328934.8407
52.3549-0.9935-0.16441.9297-0.25831.8266-0.3069-0.6458-0.2790.28230.12530.2422-0.03460.10630.1260.18030.037700.23510.07010.18886.513617.37742.5811
61.9493-0.49150.26990.6455-0.94331.8506-0.0384-0.5402-0.51490.1781-0.0040.52490.0898-0.0731-0.07240.22470.05470.02350.24970.06420.393782.935812.788543.5006
71.9251-0.3115-0.13273.64490.65071.16150.0697-0.3072-0.60370.33760.1160.23050.1147-0.1147-0.05880.1878-0.0112-0.01730.27230.06060.351574.334118.199841.9146
82.09030.0148-0.72622.0001-0.41722.37880.0041-0.25-0.00630.24260.04930.0041-0.26620.3579-0.11010.1811-0.0133-0.01060.22010.00530.164779.752930.187838.4649
92.27940.50982.20041.7114-0.32042.80650.29430.334-0.2394-0.4873-0.1460.3576-0.1684-0.2257-0.03320.28230.073-0.05470.2287-0.02610.160873.887131.957327.455
107.43475.39044.03235.44234.93686.6427-0.04910.03880.0021-0.13730.25560.67910.3179-0.2792-0.19740.56290.1021-0.31290.4477-0.09390.491466.696922.579821.1808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )A15 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 36 )A25 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 50 )A37 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )A51 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 88 )A69 - 88
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 100 )A89 - 100
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 114 )A101 - 114
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 123 )A115 - 123
10X-RAY DIFFRACTION10chain 'A' and (resid 124 through 129 )A124 - 129

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