+Open data
-Basic information
Entry | Database: PDB / ID: 3knp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of DTD from Plasmodium falciparum | ||||||
Components | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
Keywords | HYDROLASE / DTD / D-amino acid / Deacylase | ||||||
Function / homology | Function and homology information Gly-tRNA(Ala) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / tRNA binding / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å | ||||||
Authors | Manickam, Y. / Bhatt, T.K. / Sharma, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3knp.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3knp.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 3knp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3knp_validation.pdf.gz | 461.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3knp_full_validation.pdf.gz | 497.4 KB | Display | |
Data in XML | 3knp_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 3knp_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/3knp ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3knp | HTTPS FTP |
-Related structure data
Related structure data | 3knfC 3ko3C 3ko4C 3ko5C 3ko7C 3ko9C 3kobC 3kocC 3kodC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19233.084 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: dtd / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
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: 1.5418 Å / Relative weight: 1 |
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: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→19.87 Å
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||
Xplor file |
|