+Open data
-Basic information
Entry | Database: PDB / ID: 2gid | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of trypanosoma bruciei MRP1/MRP2 | ||||||
Components |
| ||||||
Keywords | TRANSLATION / T. brucei / guide RNA / matchmaking / RNA editing | ||||||
Function / homology | Function and homology information RNA modification / mRNA modification / kinetoplast / nuclear lumen / post-transcriptional regulation of gene expression / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Schumacher, M.A. / Karamooz, E. / Zikova, A. / Trantirek, L. / Lukes, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Crystal Structures of T. brucei MRP1/MRP2 Guide-RNA Binding Complex Reveal RNA Matchmaking Mechanism. Authors: Schumacher, M.A. / Karamooz, E. / Zikova, A. / Trantirek, L. / Lukes, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gid.cif.gz | 250.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gid.ent.gz | 209.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/2gid ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gid | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | MRP1/MRP2 form a heterotetramer with pseudo C4 symmetry |
-Components
#1: Protein | Mass: 22055.076 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: mrp1 / Plasmid: petduet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q952G2 #2: Protein | Mass: 21333.455 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: mrp2 / Plasmid: petduet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P90629 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: peg 3350, 0.1 M Citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→79.06 Å / Num. all: 25300 / Num. obs: 25297 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.35→3.4 Å / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→78.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4974145.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→78.84 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.35→3.51 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|