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Open data
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Basic information
Entry | Database: PDB / ID: 5wt2 | ||||||||||||
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Title | NifS from Helicobacter pylori | ||||||||||||
![]() | Cysteine desulfurase IscS | ||||||||||||
![]() | TRANSFERASE / Iron-sulfur cluster biogenesis / cysteine desulfurase | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Fujishiro, T. / Takahashi, Y. | ||||||||||||
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 | ![]() | 158.3 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 467.9 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wt4C ![]() 5zs9C ![]() 5zskC ![]() 5zsoC ![]() 5zspC ![]() 5zstC ![]() 6kfzC ![]() 6kg0C ![]() 6kg1C ![]() 1ecxS C: citing same article ( S: Starting model for refinement |
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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: V2L, 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-PLP / |
#3: Chemical | ChemComp-IPA / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES/NaOH, PEG 4000, glycerol, isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 20, 2016 |
Radiation | Monochromator: Si 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: 2.3→43.553 Å / Num. obs: 32281 / % possible obs: 98.45 % / Observed criterion σ(I): -3 / Redundancy: 7.44 % / Biso Wilson estimate: 48.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0739 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.0769 / Χ2: 1.025 / Net I/σ(I): 24.34 / Num. measured all: 448717 / Scaling rejects: 3318 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 7.614 % / Rmerge(I) obs: 0.8207 / Mean I/σ(I) obs: 3.78 / Num. measured obs: 46203 / Num. possible: 7306 / Num. unique obs: 3195 / CC1/2: 0.97 / Rpim(I) all: 0.2234 / Rrim(I) all: 0.851 / % possible all: 99.72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ECX Resolution: 2.301→43.553 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.25 / 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 max: 195.67 Å2 / Biso mean: 81.4879 Å2 / Biso min: 29.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→43.553 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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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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