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- PDB-7ysk: Crystal structure of D-Cysteine desulfhydrase from Pectobacterium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ysk | ||||||
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Title | Crystal structure of D-Cysteine desulfhydrase from Pectobacterium atrosepticum | ||||||
![]() | D-Cysteine desulfhydrase | ||||||
![]() | LYASE / PLP-dependent enzyme / D-Cysteine desulfhydrase / geminal diamine | ||||||
Function / homology | 1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / metabolic process / Putative 1-aminocyclopropane-1-carboxylate deaminase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Wang, L. / Xu, X. / Xing, X. / Zhou, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization and structural basis of D-cysteine desulfhydrase from Pectobacterium atrosepticum Authors: Xu, X. / Yang, L. / Zhang, X. / Xing, X. / Zhou, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.6 KB | Display | ![]() |
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PDB format | ![]() | 117.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.7 KB | Display | ![]() |
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Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 44.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yslC ![]() 4d97S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 39965.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA1531 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.77 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG6000, 100 mM MES/sodium hydroxide pH 6.0, 200 mM ammonium chloride |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.87 Å / Num. obs: 55529 / % possible obs: 98 % / Redundancy: 5.3 % / Biso Wilson estimate: 17.01 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3320 / CC1/2: 0.764 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D97 Resolution: 1.8→37.65 Å / SU ML: 0.2429 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1119 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.65 Å
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Refine LS restraints |
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LS refinement shell |
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