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- PDB-5cky: Crystal Structure of the MTERF1 R162A substitution bound to the t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cky | |||||||||||||||
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Title | Crystal Structure of the MTERF1 R162A substitution bound to the termination sequence. | |||||||||||||||
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![]() | TRANSCRIPTION/DNA / Protein-DNA / Transcription Factor / Mitochondria / Termination / TRANSCRIPTION-DNA complex | |||||||||||||||
Function / homology | ![]() termination of mitochondrial transcription / Mitochondrial transcription termination / DNA geometric change / mitochondrial nucleoid / DNA-templated transcription termination / Transcriptional activation of mitochondrial biogenesis / double-stranded DNA binding / nucleic acid binding / mitochondrial matrix / regulation of DNA-templated transcription ...termination of mitochondrial transcription / Mitochondrial transcription termination / DNA geometric change / mitochondrial nucleoid / DNA-templated transcription termination / Transcriptional activation of mitochondrial biogenesis / double-stranded DNA binding / nucleic acid binding / mitochondrial matrix / regulation of DNA-templated transcription / mitochondrion / RNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
Model details | R162A | |||||||||||||||
![]() | Byrnes, J. / Hauser, K. / Norona, L. / Mejia, E. / Simmerling, C. / Garcia-Diaz, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion. Authors: Byrnes, J. / Hauser, K. / Norona, L. / Mejia, E. / Simmerling, C. / Garcia-Diaz, M. #1: ![]() Title: Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription. Authors: Yakubovskaya, E. / Mejia, E. / Byrnes, J. / Hambardjieva, E. / Garcia-Diaz, 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 | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5co0C ![]() 5crjC ![]() 5crkC ![]() 3mvaS 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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Unit cell |
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Components
#1: Protein | Mass: 37125.066 Da / Num. of mol.: 1 / Fragment: UNP residues 57-396 / Mutation: R162A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 6678.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 6825.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Sodium Acetate, 0.1M Tris HCl, 15.5% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.615→79.55 Å / Num. obs: 19776 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.615→2.624 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MVA Resolution: 2.62→79.55 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.867 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.49 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 124.44 Å2 / Biso mean: 53.18 Å2 / Biso min: 27.84 Å2
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Refinement step | Cycle: final / Resolution: 2.62→79.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.615→2.683 Å / Total num. of bins used: 20
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