+Open data
-Basic information
Entry | Database: PDB / ID: 7bcu | ||||||
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Title | The adduct of NAMI-A with Hen Egg White Lysozyme at 1.5 hours. | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Ru(III) / NAMI-A / anti-cancer / adduct / HEWL | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å | ||||||
Authors | Chiniadis, L. / Giastas, P. / Bratsos, I. / Papakyriakou, A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2021 Title: Insights into the Protein Ruthenation Mechanism by Antimetastatic Metallodrugs: High-Resolution X-ray Structures of the Adduct Formed between Hen Egg-White Lysozyme and NAMI-A at Various Time Points. Authors: Chiniadis, L. / Giastas, P. / Bratsos, I. / Papakyriakou, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bcu.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bcu.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bcu_validation.pdf.gz | 879.4 KB | Display | wwPDB validaton report |
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Full document | 7bcu_full_validation.pdf.gz | 879.8 KB | Display | |
Data in XML | 7bcu_validation.xml.gz | 10 KB | Display | |
Data in CIF | 7bcu_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/7bcu ftp://data.pdbj.org/pub/pdb/validation_reports/bc/7bcu | HTTPS FTP |
-Related structure data
Related structure data | 7bcxC 7bd0C 7bdmC 193lS 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 6 types, 229 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: NACL 0.7-1.5 M, 0.1 M NA ACETATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→33.853 Å / Num. obs: 65524 / % possible obs: 99.28 % / Redundancy: 23 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06844 / Net I/σ(I): 27.98 |
Reflection shell | Resolution: 0.98→1.015 Å / Rmerge(I) obs: 0.1792 / Mean I/σ(I) obs: 3.69 / Num. unique obs: 6106 / CC1/2: 0.923 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 0.98→31.02 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→31.02 Å
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Refine LS restraints |
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LS refinement shell |
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