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Yorodumi- PDB-5jvx: X-ray structure of the adduct formed in the reaction between thau... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jvx | ||||||
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Title | X-ray structure of the adduct formed in the reaction between thaumatin and a gold carbene compound | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Bioconjug.Chem. / Year: 2016 Title: First Crystal Structure for a Gold Carbene-Protein Adduct. Authors: Ferraro, G. / Gabbiani, C. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jvx.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jvx.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jvx ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jvx | HTTPS FTP |
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-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
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-6O0 / ( #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.2 M sodium tartrate pH 7.2, 20 % polyethylene glycol |
-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: Dec 21, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→57.91 Å / Num. obs: 27058 / % possible obs: 93 % / Redundancy: 20.9 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 37 |
Reflection shell | Highest resolution: 1.7 Å / Rmerge(I) obs: 1.74 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.59 / Rpim(I) all: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QY5 Resolution: 1.7→54.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.899 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.093 / 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: 23.949 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→54.03 Å
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Refine LS restraints |
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