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Yorodumi- PDB-6goh: X-ray structure of the adduct formed upon reaction of lysozyme wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6goh | |||||||||
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Title | X-ray structure of the adduct formed upon reaction of lysozyme with a Pt(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / protein-metallodrug interaction / platinum-based drug / N-pyridylbenzimidazole bidentate ligands / stacking / non covalent bond | |||||||||
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 | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | |||||||||
Authors | Merlino, A. / Ferraro, G. | |||||||||
Citation | Journal: Dalton Trans / Year: 2018 Title: Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography. Authors: Ferraro, G. / Mansour, A.M. / Merlino, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6goh.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6goh.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 6goh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6goh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6goh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6goh_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6goh_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/6goh ftp://data.pdbj.org/pub/pdb/validation_reports/go/6goh | HTTPS FTP |
-Related structure data
Related structure data | 6gobC 6goiC 6gojC 6gokC 1dpxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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, 77 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.4 0.6 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→55.41 Å / Num. obs: 4616 / % possible obs: 99.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.43→2.48 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 226 / CC1/2: 0.644 / % possible all: 97 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DPX Resolution: 2.43→55.41 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.87 / SU B: 12.76 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.586 Å2
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Refinement step | Cycle: 1 / Resolution: 2.43→55.41 Å
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