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Open data
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Basic information
Entry | Database: PDB / ID: 3knp | ||||||
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Title | Crystal structure of DTD from Plasmodium falciparum | ||||||
![]() | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
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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 | ![]() | 189.2 KB | Display | ![]() |
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PDB format | ![]() | 152.1 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 ![]() 3ko3C ![]() 3ko4C ![]() 3ko5C ![]() 3ko7C ![]() 3ko9C ![]() 3kobC ![]() 3kocC ![]() 3kodC 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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1 | ![]()
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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, ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
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-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: Apr 10, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.3→50 Å / Num. obs: 15063 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.424 / Num. unique all: 1497 / % possible all: 96.5 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PfDTD-Iodide SAD model (not deposited) Resolution: 3.3→19.87 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 0.4 / Data cutoff high absF: 1519712 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 16.666 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.36 Å2 / Biso mean: 69.936 Å2 / Biso min: 0.01 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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