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- PDB-2fwh: atomic resolution crystal structure of the C-terminal domain of t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fwh | ||||||
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Title | atomic resolution crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (reduced form at pH7) | ||||||
![]() | Thiol:disulfide interchange protein dsbD | ||||||
![]() | OXIDOREDUCTASE / DSBD / THIOREDOXIN-LIKE / C-terminal domain / reduced form at pH7 | ||||||
Function / homology | ![]() protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / response to copper ion / protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stirnimann, C.U. / Rozhkova, A. / Grauschopf, U. / Boeckmann, R.A. / Glockshuber, R. / Capitani, G. / Gruetter, M.G. | ||||||
![]() | ![]() Title: High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study Authors: Stirnimann, C.U. / Rozhkova, A. / Grauschopf, U. / Boeckmann, R.A. / Glockshuber, R. / Capitani, G. / Gruetter, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fweC ![]() 2fwfC ![]() 2fwgC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 15097.932 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain, Residues 419-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 28.110168 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M ammonium acetate, 0.2M sodium acetate, 0.1M sodium iodide, 40% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 5, 2004 / Details: dynamically bendable mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8555 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→20 Å / Num. obs: 58388 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 6.196 Å2 / Rsym value: 0.079 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 0.99→1.03 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.445 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: modified version of 2TRX (see publication) Resolution: 0.99→15 Å / Num. parameters: 12144 / Num. restraintsaints: 17930 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 60 / Occupancy sum hydrogen: 901.7 / Occupancy sum non hydrogen: 1107.68 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→15 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 0.99 Å
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