[English] 日本語

- PDB-3bam: RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE ION... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3bam | ||||||
---|---|---|---|---|---|---|---|
Title | RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX) | ||||||
![]() |
| ||||||
![]() | HYDROLASE/DNA / HYDROLASE / PHOSPHODIESTERASE / COMPLEX (ENDONUCLEASE-DNA) / NUCLEASE / PROTEIN/DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Viadiu, H. / Aggarwal, A.K. | ||||||
![]() | ![]() Title: The role of metals in catalysis by the restriction endonuclease BamHI. Authors: Viadiu, H. / Aggarwal, A.K. #1: ![]() Title: Structure of Bam Hi Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding Authors: Newman, M. / Strzelecka, T. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2bamC ![]() 1bhmS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO BAMHI MONOMERS (CHAINS A AND B) BOUND TO A PALINDROMIC 12 BASE PAIR DNA COMPLEX. |
-
Components
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 3661.416 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 1205.841 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2410.618 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 2 molecules AB
#4: Protein | Mass: 24602.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CRYSTAL GROWN IN THE PRESENCE OF MANGANESE IONS. / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P23940, type II site-specific deoxyribonuclease |
---|
-Non-polymers , 2 types, 354 molecules 


#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | THE C-TERMINALS ARE ASYMMETRIC |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % / Description: CRYSTAL WAS ISOMORPHOUS TO 1BHM. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.3 Details: pH 5.3 CATALYSIS OCCURRED IN THE CRYSTAL AFTER SOAKING MANGANESE ION. THE ACTIVE SITE OF THE R SUBUNIT CLEAVED THE ORIGINAL D STRAND IN TWO (D AND E) RESULTING IN A POST-REACTIVE COMPLEX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 40212 / % possible obs: 72 % / Observed criterion σ(I): 0 / Redundancy: 2.77 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.09 |
Reflection | *PLUS Num. measured all: 111430 |
Reflection shell | *PLUS % possible obs: 45.6 % / Rmerge(I) obs: 0.318 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1BHM Resolution: 1.8→8 Å / Rfactor Rfree error: 0 / Cross valid method: R-FREE / σ(F): 2 Details: THE MANGANESE METALS WERE BOUND ONLY IN ONE ACTIVE SITE OF THE DIMER (THE R-SUBUNIT).
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|