[English] 日本語
Yorodumi- PDB-6ar3: Structure of a Thermostable Group II Intron Reverse Transcriptase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ar3 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (RT/Duplex (Se-Met)) | ||||||
Components |
| ||||||
Keywords | RNA binding protein/RNA/DNA / Polymerase / RNA binding protein-RNA-DNA complex | ||||||
Function / homology | Function and homology information RNA-directed DNA polymerase activity / defense response to virus / RNA binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å | ||||||
Authors | Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications. Authors: Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ar3.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ar3.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ar3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/6ar3 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6ar3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ar1C 6ar5C 3kylS 5irfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
|
-Components
#1: Protein | Mass: 50133.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: trt / Production host: Escherichia coli (E. coli) / References: UniProt: E2GM63 #2: DNA chain | Mass: 3303.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: RNA chain | Mass: 4457.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection twin |
| ||||||||||||||||||||||||
Reflection | Resolution: 3.41→48.93 Å / Num. obs: 17494 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.087 / Rrim(I) all: 0.24 / Net I/σ(I): 9.2 / Num. measured all: 132418 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KYL, 5IRF Resolution: 3.41→48.93 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.84 / SU B: 34.161 / SU ML: 0.548 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : REFINED INDIVIDUALLY Twin refinement in Refmac5 with twin fraction=0.5 and twin operator=h+2*l,-k,-l.
| |||||||||||||||||||||||||||||||||||||||||||||
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: 198.59 Å2 / Biso mean: 96.135 Å2 / Biso min: 32.35 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.41→48.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.411→3.499 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|