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- PDB-7e6c: Crystal structure of L-cycloserine-bound form of cysteine desulfu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e6c | ||||||
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Title | Crystal structure of L-cycloserine-bound form of cysteine desulfurase SufS C361A 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 | ![]() | 186.5 KB | Display | ![]() |
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PDB format | ![]() | 146.5 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 ![]() 7ceqC ![]() 7cerC ![]() 7cesC ![]() 7cetC ![]() 7ceuC ![]() 7e6aC ![]() 7e6bC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46554.520 Da / Num. of mol.: 1 / Mutation: C361A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 265 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/7TS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/7TS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-7TS / ( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.26 % |
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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 EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.73→46.44 Å / Num. obs: 67513 / % possible obs: 100 % / Redundancy: 18.821 % / Biso Wilson estimate: 39.397 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.055 / Χ2: 1.066 / Net I/σ(I): 28.77 / Num. measured all: 1270688 / Scaling rejects: 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZS9 Resolution: 1.73→46.44 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.888 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 max: 140.15 Å2 / Biso mean: 38.989 Å2 / Biso min: 20.79 Å2
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Refinement step | Cycle: final / Resolution: 1.73→46.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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