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- PDB-4d8w: Salmonella typhimurium D-Cysteine desulfhydrase soaked with D-cys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d8w | |||||||||
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Title | Salmonella typhimurium D-Cysteine desulfhydrase soaked with D-cys shows pyruvate bound 4 A away from active site | |||||||||
![]() | D-Cysteine desulfhydrase | |||||||||
![]() | LYASE / Fold type II PLP-dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily | |||||||||
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 | ![]() | 269.2 KB | Display | ![]() |
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PDB format | ![]() | 214.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 508.9 KB | Display | ![]() |
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Full document | ![]() | 519.9 KB | Display | |
Data in XML | ![]() | 54.7 KB | Display | |
Data in CIF | ![]() | 77.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d8tSC ![]() 4d8uC ![]() 4d92C ![]() 4d96C ![]() 4d97C ![]() 4d99C ![]() 4d9bC ![]() 4d9cC ![]() 4d9eC ![]() 4d9fC 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36778.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 761 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.63 % |
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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% Benzamididne, 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 26, 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→48.38 Å / Num. obs: 85215 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.013 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.6 / Num. unique all: 11081 / % possible all: 87.9 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4D8T Resolution: 2.01→48.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.908 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.161 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.264 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→48.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.005→2.057 Å / Total num. of bins used: 20
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