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Yorodumi- PDB-2e7p: Crystal structure of the holo form of glutaredoxin C1 from populu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e7p | ||||||
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Title | Crystal structure of the holo form of glutaredoxin C1 from populus tremula x tremuloides | ||||||
Components | Glutaredoxin | ||||||
Keywords | ELECTRON TRANSPORT / THIOREDOXIN FOLD / GLUTAREDOXIN / POPLAR | ||||||
Function / homology | Function and homology information glutathione disulfide oxidoreductase activity / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Populus tremula x Populus tremuloides (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Unno, H. / Takahashi, T. / Kawakami, T. / Aimoto, S. / Hase, T. / Kusunoki, M. / Rouhier, N. / Jacquot, J.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Functional, structural, and spectroscopic characterization of a glutathione-ligated [2Fe-2S] cluster in poplar glutaredoxin C1 Authors: Rouhier, N. / Unno, H. / Bandyopadhyay, S. / Masip, L. / Kim, S.K. / Hirasawa, M. / Gualberto, J.M. / Lattard, V. / Kusunoki, M. / Knaff, D.B. / Georgiou, G. / Hase, T. / Johnson, M.K. / Jacquot, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e7p.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e7p.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 2e7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/2e7p ftp://data.pdbj.org/pub/pdb/validation_reports/e7/2e7p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12435.191 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus tremula x Populus tremuloides (plant) Plasmid: PET-3D / Production host: Escherichia coli (E. coli) / References: UniProt: Q5PSJ1 #2: Chemical | ChemComp-FES / | #3: Chemical | ChemComp-GSH / #4: 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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG6000, 0.1M CITRIC ACID, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 28968 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.062 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.345 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→24.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.558 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.617 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→24.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.102→2.157 Å / Total num. of bins used: 20
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