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- PDB-6kg1: NifS from Helicobacter pylori, soaked with L-cysteine for 180 sec -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kg1 | ||||||
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Title | NifS from Helicobacter pylori, soaked with L-cysteine for 180 sec | ||||||
![]() | Cysteine desulfurase IscS | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, R. / Takahashi, Y. / Fujishiro, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes. Authors: Nakamura, R. / Hikita, M. / 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 | ![]() | 161 KB | Display | ![]() |
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PDB format | ![]() | 125.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wt2SC ![]() 5wt4C ![]() 5zs9C ![]() 5zskC ![]() 5zsoC ![]() 5zspC ![]() 5zstC ![]() 6kfzC ![]() 6kg0C 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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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.) ![]() ![]() Strain: ATCC 700392 / 26695 / Gene: iscS, HP_0220 / Production host: ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-IPA / ![]() |
#3: Chemical | ChemComp-CL / ![]() |
#4: Chemical | ChemComp-PDA / |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.22 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 17% (w/v) PEG 4000, 8.5% (v/v) 2-propanol, 15% (v/v) glycerol, 85mM HEPES-NaOH |
-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 / Details: Si(111) double crystal monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→49.18 Å / Num. obs: 20267 / % possible obs: 100 % / Redundancy: 7.086 % / Biso Wilson estimate: 73.219 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 1.019 / Net I/σ(I): 14.18 / Num. measured all: 265780 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5WT2 Resolution: 2.7→49.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.207 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.243 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.99 Å2 / Biso mean: 92.068 Å2 / Biso min: 38.4 Å2
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Refinement step | Cycle: final / Resolution: 2.7→49.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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