+Open data
-Basic information
Entry | Database: PDB / ID: 5l4r | ||||||
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Title | X-ray structure of the adduct between thaumatin and cisplatin | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / cisplatin / drug / model protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Russo Krauss, I. / Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2016 Title: Cisplatin-Protein Interactions: Unexpected Drug Binding to N-Terminal Amine and Lysine Side Chains. Authors: Russo Krauss, I. / Ferraro, G. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l4r.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l4r.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 5l4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l4r_validation.pdf.gz | 850.7 KB | Display | wwPDB validaton report |
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Full document | 5l4r_full_validation.pdf.gz | 856.1 KB | Display | |
Data in XML | 5l4r_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5l4r_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/5l4r ftp://data.pdbj.org/pub/pdb/validation_reports/l4/5l4r | HTTPS FTP |
-Related structure data
Related structure data | 3qy5S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Escherichia coli (E. coli) / References: UniProt: P02883 |
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-Non-polymers , 5 types, 437 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CPT / #5: Chemical | ChemComp-GOL / | #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: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 % PEG3350, 0.2 M sodium tartrate. Crystals of the adduct were obtained by soaking procedure, adding 1 uL of cisplatin solution 10 mM to the drop containing thaumatin crystals |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→53.98 Å / Num. obs: 43868 / % possible obs: 94.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.7 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QY5 Resolution: 1.45→53.97 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.966 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.169 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→53.97 Å
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Refine LS restraints |
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