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- PDB-7ceq: Crystal structure of cysteine desulfurase SufS H121A from Bacillu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ceq | ||||||
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Title | Crystal structure of cysteine desulfurase SufS H121A from Bacillus subtilis | ||||||
![]() | Cysteine desulfurase SufS | ||||||
![]() | BIOSYNTHETIC PROTEIN / cysteine desulfurase / PLP-dependent enzyme / cysteine metabolism / cycloserine / inhibitor / Fe-S cluster biosynthesis | ||||||
Function / homology | ![]() cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, R. / Takahashi, Y. / Fujishiro, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms. Authors: Nakamura, R. / Ogawa, S. / Takahashi, Y. / Fujishiro, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.7 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kfyC ![]() 7ceoC ![]() 7cepC ![]() 7cerC ![]() 7cesC ![]() 7cetC ![]() 7ceuC ![]() 7e6aC ![]() 7e6bC ![]() 7e6cC ![]() 7e6dC ![]() 7e6eC ![]() 7e6fC ![]() 5zs9S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46616.430 Da / Num. of mol.: 1 / Mutation: H121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Tris-HCl, 50 mM Lithium sulfate, 50%(v/v) PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Monochromator: Numerical link type 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: 2→43.52 Å / Num. obs: 43589 / % possible obs: 100 % / Redundancy: 20.14 % / Biso Wilson estimate: 41.91 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 19.52 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 3.86 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZS9 Resolution: 2→43.52 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.58 / Stereochemistry target values: ML
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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: 44.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.52 Å
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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