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Open data
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Basic information
Entry | Database: PDB / ID: 6kil | ||||||
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Title | N21Q mutant thioredoxin from Halobacterium salinarum NRC-1 | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE / halophile | ||||||
Function / homology | ![]() oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Arai, S. / Shibazaki, C. / Shimizu, R. / Adachi, M. / Ishibashi, M. / Tokunaga, H. / Tokunaga, M. | ||||||
![]() | ![]() Title: Catalytic mechanism and evolutional characteristics of thioredoxin from Halobacterium salinarum NRC-1. Authors: Arai, S. / Shibazaki, C. / Shimizu, R. / Adachi, M. / Ishibashi, M. / Tokunaga, H. / Tokunaga, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.6 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e0qS 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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Unit cell |
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Components
#1: Protein | Mass: 13186.258 Da / Num. of mol.: 1 / Mutation: N21Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: trxA, trxA1_1, trxA1_2, VNG_6073G, VNG_6453G / Plasmid: pCold-I / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl buffer (pH8.5), 2.0 M ammonium sulfate, 12.7 mg/mL of protein PH range: 8 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2015 |
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 13317 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Χ2: 1.79 / Net I/av σ(I): 12.9 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.383 / Num. unique obs: 647 / CC1/2: 0.939 / Rpim(I) all: 0.154 / Rrim(I) all: 0.413 / Χ2: 1.345 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E0Q Resolution: 1.6→32.71 Å / SU ML: 0.0745 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.3461
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→32.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 32.8646478415 Å / Origin y: 26.4296171813 Å / Origin z: 22.4906493733 Å
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Refinement TLS group | Selection details: all |