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- PDB-4d9f: D-Cysteine desulfhydrase from Salmonella typhimurium complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d9f | ||||||
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Title | D-Cysteine desulfhydrase from Salmonella typhimurium complexed with D-cycloserine (DCS) | ||||||
![]() | D-Cysteine desulfhydrase | ||||||
![]() | LYASE / Fold type II PLP-dependent enzyme / tryptophan synthase beta subunit like family | ||||||
Function / homology | ![]() D-cysteine desulfhydrase / D-amino acid metabolic process / D-cysteine desulfhydrase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bharath, S.R. / Shveta, B. / Rajesh, K.H. / Savithri, H.S. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase. Authors: Bharath, S.R. / Bisht, S. / Harijan, R.K. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.5 KB | Display | ![]() |
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PDB format | ![]() | 198.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 47.7 KB | Display | |
Data in CIF | ![]() | 64.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d8tSC ![]() 4d8uC ![]() 4d8wC ![]() 4d92C ![]() 4d96C ![]() 4d97C ![]() 4d99C ![]() 4d9bC ![]() 4d9cC ![]() 4d9eC 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: 36550.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DCS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1.5M Ammonium sulphate, 15% (v/v) ethylene glycol, 0.1M HEPES, 0.2% Benzamidine, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2010 / Details: mirrors |
Radiation | Monochromator: Ni mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→58.78 Å / Num. obs: 32824 / % possible obs: 83 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4 / Num. unique all: 3868 / % possible all: 66.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D8T Resolution: 2.61→58.74 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.85 / SU B: 15.286 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.769 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→58.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.613→2.681 Å / Total num. of bins used: 20
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