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Yorodumi- PDB-1nw6: Structure of the beta class N6-adenine DNA methyltransferase RsrI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nw6 | ||||||
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Title | Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to sinefungin | ||||||
Components | MODIFICATION METHYLASE RSRI | ||||||
Keywords | TRANSFERASE / ADENINE DNA METHYLTRANSFERASE / SINEFUNGIN / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Thomas, C.B. / Scavetta, R.D. / Gumport, R.I. / Churchill, M.E.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding Authors: Thomas, C.B. / Scavetta, R.D. / Gumport, R.I. / Churchill, M.E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nw6.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nw6.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nw6 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nw6 | HTTPS FTP |
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-Related structure data
Related structure data | 1nw5C 1nw7C 1nw8C 1eg2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | the other half of the putative dimer is related by a 2-fold rotation about the y axis |
-Components
#1: Protein | Mass: 35702.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: rsrIM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14751, site-specific DNA-methyltransferase (adenine-specific) | ||||
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#2: Chemical | #3: Chemical | ChemComp-SFG / | #4: 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: 2.16 Å3/Da / Density % sol: 42.93 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: lithium sulfate, HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→28 Å / Num. all: 23315 / Num. obs: 23268 / % possible obs: 99.8 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.038 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.94→2.01 Å / Mean I/σ(I) obs: 6.5 / Num. unique all: 2292 / Rsym value: 0.167 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 78952 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS Num. possible: 7600 / Num. unique obs: 2292 / Num. measured obs: 99.8 / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EG2 Resolution: 1.94→28.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 885171.71 / Data cutoff high rms absF: 885171.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.2848 Å2 / ksol: 0.366466 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→28.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 28 Å / Num. reflection obs: 23268 / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 / Rfactor Rwork: 0.25 / Num. reflection Rwork: 2292 |