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Yorodumi- PDB-4uwv: Lysozyme soaked with a ruthenium based CORM with a pyridine ligan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uwv | ||||||
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Title | Lysozyme soaked with a ruthenium based CORM with a pyridine ligand (complex 8) | ||||||
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: 1.77 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 | 4uwv.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uwv.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uwv_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 4uwv_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 4uwv_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 4uwv_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uwv ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uwv | HTTPS FTP |
-Related structure data
Related structure data | 4uwnC 4uwuC 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 natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 131 molecules
#2: Chemical | ChemComp-CL / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Chemical | ChemComp-CMO / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % / 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: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 18, 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: 1.77→27.26 Å / Num. obs: 11793 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.77→1.86 Å / Redundancy: 13.2 % / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.77→27.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.551 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 23.687 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→27.26 Å
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