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- PDB-7cet: Crystal structure of D-cycloserine-bound form of cysteine desulfu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cet | ||||||
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Title | Crystal structure of D-cycloserine-bound form of cysteine desulfurase NifS from Helicobacter pylori | ||||||
![]() | Cysteine desulfurase IscS | ||||||
![]() | 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 / [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. / 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 | ![]() | 158 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 843.8 KB | Display | ![]() |
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Full document | ![]() | 853.1 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kfyC ![]() 7ceoC ![]() 7cepC ![]() 7ceqC ![]() 7cerC ![]() 7cesC ![]() 7ceuC ![]() 7e6aC ![]() 7e6bC ![]() 7e6cC ![]() 7e6dC ![]() 7e6eC ![]() 7e6fC ![]() 5wt2S 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: 44125.230 Da / Num. of mol.: 1 / Mutation: L2V, K138R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-IPA / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-7TS / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085 M Sodium HEPES, 17% (w/v) PEG 4000, 8.5% (v/v) Isopropyl alcohol, 15% (v/v) Glycerol |
-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: Jun 29, 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: 2.64→48.14 Å / Num. obs: 21427 / % possible obs: 97.97 % / Redundancy: 3.966 % / Biso Wilson estimate: 66.93 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05187 / Rpim(I) all: 0.0202 / Rrim(I) all: 0.05594 / Χ2: 1.148 / Net I/σ(I): 25.38 / Num. measured all: 156707 / Scaling rejects: 171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WT2 Resolution: 2.64→48.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.765 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.245 / 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: 192.45 Å2 / Biso mean: 78.403 Å2 / Biso min: 40.18 Å2
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Refinement step | Cycle: final / Resolution: 2.64→48.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.708 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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