[English] 日本語
Yorodumi- PDB-6jre: Structure of N-terminal domain of Plasmodium vivax p43 (PfNTD) so... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jre | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of N-terminal domain of Plasmodium vivax p43 (PfNTD) solved by Co-SAD phasing | ||||||
Components | Aminoacyl-tRNA synthetase-interacting multifunctional protein p43 | ||||||
Keywords | LIGASE / GST-like domain / AIMP1 / Plasmodium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å | ||||||
Authors | Manickam, Y. / Harlos, K. / Sharma, M. / Gupta, S. / Sharma, A. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein. Authors: Gupta, S. / Chhibber-Goel, J. / Sharma, M. / Parvez, S. / Harlos, K. / Sharma, A. / Yogavel, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jre.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jre.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/6jre ftp://data.pdbj.org/pub/pdb/validation_reports/jr/6jre | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21811.281 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVC01_120068600, PVP01_1264700, PVT01_120069000 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1G4HHT8, UniProt: A0A0J9VJU0*PLUS |
---|---|
#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2M sodium bromide, 5% ethyl acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.59 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.59 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→61.8 Å / Num. obs: 6539 / % possible obs: 95.8 % / Redundancy: 58.1 % / CC1/2: 1 / Rrim(I) all: 0.081 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.59→2.63 Å / Redundancy: 28.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 241 / CC1/2: 0.7 / Rrim(I) all: 3.353 / % possible all: 71.8 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing dm | FOM : 0.65 / FOM acentric: 0.64 / FOM centric: 0.66 / Reflection: 6429 / Reflection acentric: 5225 / Reflection centric: 1204 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.59→61.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.958 / SU B: 43.464 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.983 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||
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: 215.14 Å2 / Biso mean: 114.55 Å2 / Biso min: 64.54 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.59→61.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.59→2.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 18.564 Å / Origin y: 27.139 Å / Origin z: 12.174 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|