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Yorodumi- PDB-5dma: Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dma | ||||||||||||
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Title | Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase | ||||||||||||
Components | ATP-dependent DNA helicase PcrA | ||||||||||||
Keywords | HYDROLASE / RNA polymerase / PcrA/UvrD helicase / Tudor domain / Transcription | ||||||||||||
Function / homology | Function and homology information DNA 3'-5' helicase / DNA unwinding involved in DNA replication / isomerase activity / DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.53 Å | ||||||||||||
Authors | Lin, C.L. / Dillingham, M. / Wigley, D. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: The structure and function of an RNA polymerase interaction domain in the PcrA/UvrD helicase. Authors: Sanders, K. / Lin, C.L. / Smith, A.J. / Cronin, N. / Fisher, G. / Eftychidis, V. / McGlynn, P. / Savery, N.J. / Wigley, D.B. / Dillingham, M.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dma.cif.gz | 24.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dma.ent.gz | 14.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dma ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dma | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 5977.875 Da / Num. of mol.: 1 / Fragment: C-terminal tudor domain, UNP residues 671-724 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: pcrA / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / References: UniProt: P56255, DNA helicase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 9252 / % possible obs: 99.9 % / Redundancy: 10 % / Rsym value: 0.034 / Net I/σ(I): 61.6 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 7.7 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.53→29.597 Å / FOM work R set: 0.8524 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.73 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.74 Å2 / Biso mean: 16.47 Å2 / Biso min: 6.09 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→29.597 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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