+Open data
-Basic information
Entry | Database: PDB / ID: 7bdm | ||||||
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Title | The adduct of NAMI-A with Hen Egg White Lysozyme at 98 hours. | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Ru(III) / NAMI-A / HEWL / anti-cancer | ||||||
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: 1.07 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 | 7bdm.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bdm.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bdm_validation.pdf.gz | 612.6 KB | Display | wwPDB validaton report |
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Full document | 7bdm_full_validation.pdf.gz | 613.3 KB | Display | |
Data in XML | 7bdm_validation.xml.gz | 9 KB | Display | |
Data in CIF | 7bdm_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/7bdm ftp://data.pdbj.org/pub/pdb/validation_reports/bd/7bdm | HTTPS FTP |
-Related structure data
Related structure data | 7bcuC 7bcxC 7bd0C 193lS C: citing same article (ref.) S: Starting model for refinement |
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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 , 5 types, 142 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-RU / | #5: Chemical | ChemComp-EDO / | #6: 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: 2.05 Å3/Da / Density % sol: 39.89 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: NACL 1.5 M, 0.1 M NA ACETATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP |
-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: 1.07→33.928 Å / Num. obs: 48381 / % possible obs: 91.44 % / Redundancy: 16.2 % / Biso Wilson estimate: 16.08 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07433 / Rpim(I) all: 0.01835 / Net I/σ(I): 36.11 |
Reflection shell | Resolution: 1.07→1.108 Å / Redundancy: 8.8 % / Num. unique obs: 4759 / CC1/2: 0.357 / Rpim(I) all: 0.5978 / % possible all: 91.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.07→33.928 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19 / 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: 1.07→33.928 Å
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Refine LS restraints |
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LS refinement shell |
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