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Yorodumi- PDB-5ft8: Crystal structure of the complex between the cysteine desulfurase... -
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-Basic information
Entry | Database: PDB / ID: 5ft8 | |||||||||
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Title | Crystal structure of the complex between the cysteine desulfurase CsdA and the sulfur-acceptor CsdE in the persulfurated state at 2.50 Angstroem resolution | |||||||||
Components |
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Keywords | TRANSFERASE / L-CYSTEINE DESULFURASE / SULFUR ACCEPTOR / TRANSPERSULFURATION / SULFUR TRAFFICKING | |||||||||
Function / homology | Function and homology information cyclic threonylcarbamoyladenosine biosynthetic process / 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 / sulfur carrier activity / selenocysteine lyase / selenocysteine lyase activity / L-cysteine desulfurase complex ...cyclic threonylcarbamoyladenosine biosynthetic process / 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 / sulfur carrier 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 | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. ...Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C. | |||||||||
Citation | Journal: Acs Catalysis / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ft8.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ft8.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5ft8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5ft8 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ft8 | HTTPS FTP |
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-Related structure data
Related structure data | 5ft5C 5ft6C 5ft4S 5ft7 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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
-Protein , 2 types, 16 molecules ACEGIKMOQSUWYace
#1: Protein | Mass: 43434.172 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: csdA, ygdJ, b2810, JW2781 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q46925, cysteine desulfurase, Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds, selenocysteine lyase #2: Protein | Mass: 16946.336 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: csdE, ygdK, b2811, JW2782 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AGF2 |
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-Non-polymers , 4 types, 1096 molecules
#3: Chemical | ChemComp-PLP / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-GOL / #6: 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: 2.71 Å3/Da / Density % sol: 54.72 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98011 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.3 Å / Num. obs: 178722 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.5→2.63 Å / Redundancy: 1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 5FT4 AND 5FT7 Resolution: 2.5→48.3 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.889 / SU B: 30.717 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R: 0.601 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 58.429 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.3 Å
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Refine LS restraints |
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