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Yorodumi- PDB-1nw5: Structure of the beta class N6-adenine DNA methyltransferase RsrI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nw5 | ||||||
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Title | Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to S-ADENOSYLMETHIONINE | ||||||
Components | MODIFICATION METHYLASE RSRI | ||||||
Keywords | TRANSFERASE / ADENINE DNA METHYLTRANSFERASE / S-ADENOSYLMETHIONINE / 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 / methylation / DNA binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 1nw5.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nw5.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nw5_validation.pdf.gz | 682.4 KB | Display | wwPDB validaton report |
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Full document | 1nw5_full_validation.pdf.gz | 686.6 KB | Display | |
Data in XML | 1nw5_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1nw5_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nw5 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nw5 | HTTPS FTP |
-Related 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 | ChemComp-CL / |
#3: Chemical | ChemComp-SAM / |
#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: 2.13 Å3/Da / Density % sol: 42.33 % | |||||||||||||||||||||||||||||||||||
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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: 2.05→20 Å / Num. all: 19581 / Num. obs: 18235 / % possible obs: 93.2 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.028 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.05→2.09 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 681 / Rsym value: 0.295 / % possible all: 70.7 |
Reflection | *PLUS Num. measured all: 43607 / Rmerge(I) obs: 0.028 |
Reflection shell | *PLUS % possible obs: 70.7 % / Rmerge(I) obs: 0.295 / Num. unique obs: 681 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 117750.83 / Data cutoff high rms absF: 117750.83 / 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: 41.477 Å2 / ksol: 0.355505 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 18235 / % reflection Rfree: 10 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.28 / Rfactor Rwork: 0.24 / Num. reflection Rwork: 681 |