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- PDB-6ar3: Structure of a Thermostable Group II Intron Reverse Transcriptase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ar3 | ||||||
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Title | Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (RT/Duplex (Se-Met)) | ||||||
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![]() | RNA binding protein/RNA/DNA / Polymerase / RNA binding protein-RNA-DNA complex | ||||||
Function / homology | ![]() RNA-directed DNA polymerase activity / defense response to virus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.3 KB | Display | ![]() |
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PDB format | ![]() | 161.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ar1C ![]() 6ar5C ![]() 3kylS ![]() 5irfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 50133.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: trt / Production host: ![]() ![]() #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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
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 |
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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
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Processing
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Refinement | Method to determine structure: ![]() 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.
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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
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Refinement step | Cycle: final / Resolution: 3.41→48.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.411→3.499 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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