+
Open data
-
Basic information
Entry | Database: PDB / ID: 1boo | ||||||
---|---|---|---|---|---|---|---|
Title | PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC) | ||||||
![]() | PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II) | ||||||
![]() | TRANSFERASE / TYPE II DNA-(CYTOSINE N4) METHYLTRANSFERASE / AMINO METHYLATION / SELENOMETHIONINE / MULTIWAVELENGTH ANOMALOUS DIFFRACTION | ||||||
Function / homology | ![]() site-specific DNA-methyltransferase (cytosine-N4-specific) / : / : / site-specific DNA-methyltransferase (cytosine-N4-specific) activity / N-methyltransferase activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, W. / O'Gara, M. / Blumenthal, R.M. / Cheng, X. | ||||||
![]() | ![]() Title: Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Authors: Gong, W. / O'Gara, M. / Blumenthal, R.M. / Cheng, X. #1: ![]() Title: Expression, Purification, Mass Spectrometry, Crystallization and Multiwavelength Anomalous Diffraction of Selenomethionyl PvuII DNA Methyltransferase (Cytosine-N4-Specific) Authors: O'Gara, M. / Adams, G.M. / Gong, W. / Kobayashi, R. / Blumenthal, R.M. / Cheng, X. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.6975, -0.6041, 0.3855), Vector: |
-
Components
#1: Protein | Mass: 36956.207 Da / Num. of mol.: 1 Fragment: STARTING FROM THE INTERNAL TRANSLATION INITIATOR AT MET14 Mutation: N TERMIANL DELETION (RESIDUES 1-13) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): DH10B References: UniProt: P11409, site-specific DNA-methyltransferase (cytosine-N4-specific) |
---|---|
#2: Chemical | ChemComp-SAH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 38.2 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.2 Details: 0.1 M HEPES PH 7.2, 0.2 M SODIUM ACETATE 20% POLYETHYLENE GLYCOL 400 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 289 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. obs: 14886 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.5 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 5.5 / % possible all: 97.5 | |||||||||||||||
Reflection | *PLUS Num. measured all: 54787 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.5 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|