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Yorodumi- PDB-2eio: Design of Disulfide-linked Thioredoxin Dimers and Multimers Throu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eio | ||||||
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Title | Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts | ||||||
Components | Thioredoxin 1 | ||||||
Keywords | ELECTRON TRANSPORT / THIOREDOXIN / MUTANT / DI-SULFIDE BOND | ||||||
Function / homology | Function and homology information DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kobayashi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts Authors: Das, M. / Kobayashi, M. / Yamada, Y. / Sreeramulu, S. / Ramakrishnan, C. / Wakatsuki, S. / Kato, R. / Varadarajan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eio.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eio.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 2eio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/2eio ftp://data.pdbj.org/pub/pdb/validation_reports/ei/2eio | HTTPS FTP |
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-Related structure data
Related structure data | 2eiqC 2eirC 2trxS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 11661.417 Da / Num. of mol.: 4 / Mutation: E101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25 #2: 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: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 3350, 0.1M TRIS, 0.2M MAGNESIUM CHLORIDE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2005 / Details: MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 14472 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.258 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TRX Resolution: 2.6→38.58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 148038.94 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.8641 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→38.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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