+Open data
-Basic information
Entry | Database: PDB / ID: 4boc | ||||||
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Title | Structure of mitochondrial RNA polymerase elongation complex | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA POLYMERASE / MITOCHONDRIA / TRANSFERASE / DNA-RNA HYBRID | ||||||
Function / homology | Function and homology information Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / transcription initiation at mitochondrial promoter / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription / DNA primase activity / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / transcription initiation at mitochondrial promoter / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription / DNA primase activity / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / mitochondrial matrix / protein-containing complex / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Schwinghammer, K. / Cheung, A. / Morozov, Y. / Agaronyan, K. / Temiakov, D. / Cramer, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structure of Human Mitochondrial RNA Polymerase Elongation Complex Authors: Schwinghammer, K. / Cheung, A.C.M. / Morozov, Y.I. / Agaronyan, K. / Temiakov, D. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4boc.cif.gz | 487.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4boc.ent.gz | 394.8 KB | Display | PDB format |
PDBx/mmJSON format | 4boc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4boc_validation.pdf.gz | 476 KB | Display | wwPDB validaton report |
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Full document | 4boc_full_validation.pdf.gz | 487.7 KB | Display | |
Data in XML | 4boc_validation.xml.gz | 38 KB | Display | |
Data in CIF | 4boc_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/4boc ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4boc | HTTPS FTP |
-Related structure data
Related structure data | 3spaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 123384.539 Da / Num. of mol.: 1 / Fragment: RESIDUES 151-1230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O00411, DNA-directed RNA polymerase |
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#2: DNA chain | Mass: 8645.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#3: RNA chain | Mass: 4493.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#4: DNA chain | Mass: 8535.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#5: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL HIS TAG FOR PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 8% PEG 4000, 200 MM SODIUM ACETATE, 100 MM TRISODIUM CITRATE (PH=5.5), 10% GLYCEROL, 10 MM DTT, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→39.8 Å / Num. obs: 54985 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 20.7 % / Biso Wilson estimate: 90.77 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SPA Resolution: 2.65→39.81 Å / Cor.coef. Fo:Fc: 0.9549 / Cor.coef. Fo:Fc free: 0.9465 / SU R Cruickshank DPI: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.337 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.227
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Displacement parameters | Biso mean: 97.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.415 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→39.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.72 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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