+
Open data
-
Basic information
Entry | Database: PDB / ID: 7xeq | ||||||
---|---|---|---|---|---|---|---|
Title | NifS with D-cysteine | ||||||
![]() | Cysteine desulfurase IscS | ||||||
![]() | BIOSYNTHETIC PROTEIN / Cysteine desulfurase / Inhibitor | ||||||
Function / homology | ![]() cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / [2Fe-2S] cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, R. / Fujishiro, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine Authors: Nakamura, R. / Takahashi, Y. / Fujishiro, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 158.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 123.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 798.8 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xejC ![]() 7xekC ![]() 7xelC ![]() 7xenC ![]() 7xesC ![]() 5wt2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 44125.230 Da / Num. of mol.: 1 / Mutation: L2V, K138R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-IPA / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-9YX / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 85 mM HEPES-NaOH, 17% (w/v) PEG4000, 15% (v/v) glycerol, 8.5% (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 28, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.9→49.14 Å / Num. obs: 16554 / % possible obs: 99.9 % / Redundancy: 12.51 % / Biso Wilson estimate: 78.961 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.078 / Χ2: 0.928 / Net I/σ(I): 23.63 / Num. measured all: 207089 / Scaling rejects: 159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5WT2 Resolution: 2.9→49.14 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 28.294 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 225.2 Å2 / Biso mean: 102.949 Å2 / Biso min: 43.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→49.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|