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- PDB-5b7u: Apo Structure of Cysteine Desulfurase from Thermococcus onnurineu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b7u | ||||||
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Title | Apo Structure of Cysteine Desulfurase from Thermococcus onnurineus NA1 at 1.89A | ||||||
![]() | Cysteine desulfurase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ho, T.-H. / Kang, L.-W. | ||||||
![]() | ![]() Title: Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the ArchaeonThermococcus onnurineus NA1. Authors: Ho, T.-H. / Huynh, K.-H. / Nguyen, D.Q. / Park, H. / Jung, K. / Sur, B. / Ahn, Y.-J. / Cha, S.-S. / Kang, L.-W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.5 KB | Display | ![]() |
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PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5b7sSC ![]() 5b87C ![]() 5b89C 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: 46932.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: NA1 / Gene: TON_0289 / Production host: ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CYS / | ![]() #3: Chemical | ChemComp-IPA / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 1mM PLP, 5mM cystine, 10% (v/v) Isopropanol, 5% (w/v) PEG 8000, Imidazol/HCl pH 5.9 PH range: 5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. obs: 66011 / % possible obs: 97 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 54.02 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 9 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5B7S Resolution: 1.9→46.177 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.697 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.938 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.177 Å
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Refine LS restraints |
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