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Open data
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Basic information
Entry | Database: PDB / ID: 3kod | ||||||
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Title | DTD from Plasmodium falciparum in complex with D-Serine | ||||||
![]() | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() Gly-tRNA(Ala) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Manickam, Y. / Bhatt, T.K. / Sharma, A. | ||||||
![]() | ![]() Title: Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase Authors: Bhatt, T.K. / Yogavel, M. / Wydau, S. / Berwal, R. / Sharma, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.3 KB | Display | ![]() |
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PDB format | ![]() | 149.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3knfC ![]() 3knpC ![]() 3ko3C ![]() 3ko4C ![]() 3ko5C ![]() 3ko7C ![]() 3ko9C ![]() 3kobC ![]() 3kocC 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19233.084 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 3D7 / Gene: dtd / Plasmid: pET28a / Production host: ![]() ![]() ![]() References: UniProt: Q8IIS0, ![]() #2: Chemical | ChemComp-DSN / ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.58 % / Mosaicity: 0.977 ° |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.1M MES, pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6.2-6.5 |
-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: Oct 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.91→30 Å / Num. obs: 20428 / % possible obs: 97 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.101 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.566 / Num. unique all: 1858 / Χ2: 1.343 / % possible all: 89.8 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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 max: 131.54 Å2 / Biso mean: 87.581 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
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