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- PDB-5ft5: Crystal structure of the cysteine desulfurase CsdA (persulfurated... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ft5 | ||||||
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Title | Crystal structure of the cysteine desulfurase CsdA (persulfurated) from Escherichia coli at 2.384 Angstroem resolution | ||||||
![]() | L-CYSTEINE DESULFURASE CSDA | ||||||
![]() | TRANSFERASE / L-CYSTEINE DESULFURASE / SULFUR ACCEPTOR / TRANSPERSULFURATION / SULFUR TRAFFICKING | ||||||
Function / homology | ![]() sulfur compound transport / selenocysteine catabolic process / sulfur amino acid metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / L-cysteine desulfurase complex / sulfurtransferase activity / cysteine desulfurase ...sulfur compound transport / selenocysteine catabolic process / sulfur amino acid metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / L-cysteine desulfurase complex / sulfurtransferase activity / cysteine desulfurase / cysteine desulfurase activity / L-cysteine catabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. ...Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C. | ||||||
![]() | ![]() Title: Mechanism of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System Authors: Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324 KB | Display | ![]() |
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PDB format | ![]() | 266 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.8 KB | Display | ![]() |
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Full document | ![]() | 509.7 KB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ft6C ![]() 5ft8C ![]() 5ft4S ![]() 5ft7 S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.79, -0.4144, -0.4518), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43306.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q46925, cysteine desulfurase, Lyases; Carbon-sulfur lyases, selenocysteine lyase |
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-Non-polymers , 5 types, 314 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.44 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→36.72 Å / Num. obs: 29983 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 22.65 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.4 / % possible all: 91.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5FT4 Resolution: 2.384→36.721 Å / SU ML: 0.27 / σ(F): 1.9 / Phase error: 21.21 / Stereochemistry target values: ML / Details: U VALUES WITH TLS ADDED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.384→36.721 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: 21.4065 Å / Origin y: 44.2324 Å / Origin z: 17.57 Å
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Refinement TLS group | Selection details: ALL |