+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ynm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of restriction endonuclease HinP1I | ||||||
![]() | R.HinP1I restriction endonuclease | ||||||
![]() | HYDROLASE / Restriction endonuclease / dimerizaton | ||||||
Function / homology | Trna Endonuclease; Chain: A, domain 1 - #40 / Restriction endonuclease, type II, HinP1I / R.HinP1I restriction endonuclease / Trna Endonuclease; Chain: A, domain 1 / endonuclease activity / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / R.HinP1I restriction endonuclease![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Z. / Horton, J.R. / Maunus, R. / Wilson, G.G. / Roberts, R.J. / Cheng, X. | ||||||
![]() | ![]() Title: Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI Authors: Yang, Z. / Horton, J.R. / Maunus, R. / Wilson, G.G. / Roberts, R.J. / Cheng, X. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 46.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 373.7 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit of the crystal structure contain one biological unit. |
-
Components
#1: Protein | Mass: 28791.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5I6E6, type II site-specific deoxyribonuclease |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.3 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, sodium chloride, ammonium acetate, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 27, 1998 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→22 Å / Num. all: 14790 / Num. obs: 14790 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 5.1 / Num. unique all: 714 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.7455 Å2 / ksol: 0.339586 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.65→2.74 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|