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- PDB-6ar5: Structure of a Thermostable Group II Intron Reverse Transcriptase... -

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Basic information

Entry
Database: PDB / ID: 6ar5
TitleStructure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (Duplex Only)
Components
  • DNA
  • RNA
KeywordsDNA/RNA / Duplex / DNA-RNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 Å
AuthorsStamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M.
CitationJournal: 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
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA
B: RNA


Theoretical massNumber of molelcules
Total (without water)8,4162
Polymers8,4162
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-7 kcal/mol
Surface area5050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.428, 46.428, 82.195
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain DNA


Mass: 3936.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA


Mass: 4479.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium malonate, ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.41→36.118 Å / Num. obs: 4275 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.012 / Rrim(I) all: 0.055 / Net I/σ(I): 48 / Num. measured all: 88698 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.41-2.521.30.5314360.9830.1170.544100
9.02-41.1160.02110610.0060.02298.8

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.11.1refinement
PDB_EXTRACT3.22data extraction
XDSMay 1, 2016data reduction
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.413→36.118 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 212 4.99 %Random
Rwork0.1854 ---
obs0.187 4250 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.71 Å2 / Biso mean: 39.8353 Å2 / Biso min: 28.64 Å2
Refinement stepCycle: final / Resolution: 2.413→36.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 556 0 21 577
Biso mean---38.65 -
Num. residues----27
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007621
X-RAY DIFFRACTIONf_angle_d0.948959
X-RAY DIFFRACTIONf_chiral_restr0.035119
X-RAY DIFFRACTIONf_plane_restr0.00627
X-RAY DIFFRACTIONf_dihedral_angle_d10.047289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4131-3.04010.3296970.289519722069
3.0401-36.1220.17951150.15420662181

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