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- PDB-2eiq: Design of Disulfide-linked Thioredoxin Dimers and Multimers Throu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2eiq | ||||||
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Title | Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts | ||||||
![]() | Thioredoxin 1 | ||||||
![]() | ELECTRON TRANSPORT / THIOREDOXIN / MUTANT / DI-SULFIDE BOND | ||||||
Function / homology | ![]() DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kobayashi, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 41.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2eioC ![]() 2eirC ![]() 2trxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11689.427 Da / Num. of mol.: 2 / Mutation: T89C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 40% MPD, 1MM CUPRIC ACETATE, 10MM SODIUM ACETATE, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 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: 1.9→54.55 Å / Num. all: 18923 / Num. obs: 18812 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.304 / Rsym value: 0.304 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2TRX Resolution: 1.9→41.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.996 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 18.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→41.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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