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Yorodumi- PDB-4uwn: Lysozyme soaked with a ruthenium based CORM with a methione oxide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uwn | ||||||
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Title | Lysozyme soaked with a ruthenium based CORM with a methione oxide ligand (complex 6b) | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE | ||||||
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: 1.67 Å | ||||||
Authors | Santos, M.F.A. / Mukhopadhyay, A. / Romao, M.J. / Romao, C.C. / Santos-Silva, T. | ||||||
Citation | Journal: Dalton Trans / Year: 2015 Title: A Contribution to the Rational Design of Ru(Co)3Cl2L Complexes for in Vivo Delivery of Co. Authors: Seixas, J.D. / Santos, M.F.A. / Mukhopadhyay, A. / Coelho, A.C. / Reis, P.M. / Veiros, L.F. / Marques, A.R. / Penacho, N. / Goncalves, A.M.L. / Romao, M.J. / Bernardes, G.J.L. / Santos-Silva, T. / Romao, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uwn.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uwn.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uwn_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 4uwn_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 4uwn_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4uwn_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uwn ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uwn | HTTPS FTP |
-Related structure data
Related structure data | 4uwuC 4uwvC 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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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 , 6 types, 160 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-RU / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2-10% (M/V) NACL IN 0.1 M ACETATE BUFFER PH 4.5. PROTEIN STOCK CONCENTRATION OF 50 MG/ML. HANGING DROP VAPOR DIFFUSION METHOD, 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→56.52 Å / Num. obs: 14435 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 6.8 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.67→56.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.651 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→56.52 Å
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Refine LS restraints |
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