[English] 日本語
Yorodumi- PDB-5hlk: Crystal structure of the ternary EcoRV-DNA-Lu complex with cleave... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hlk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate. | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE/DNA / Hydrolase / Protein-DNA complex / Lutetium / HYDROLASE-DNA complex | |||||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Sangani, S.S. / Kehr, A.D. / Sinha, K. / Rule, G.S. / Jen-Jacobson, L. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex. Authors: Sinha, K. / Sangani, S.S. / Kehr, A.D. / Rule, G.S. / Jen-Jacobson, L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hlk.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hlk.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hlk ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hlk | HTTPS FTP |
---|
-Related structure data
Related structure data | 5f8aC 1b94S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28559.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecoRVR / Production host: Escherichia coli (E. coli) References: UniProt: P04390, type II site-specific deoxyribonuclease |
---|
-DNA chain , 2 types, 4 molecules CDEF
#2: DNA chain | Mass: 1841.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 1774.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-Non-polymers , 4 types, 252 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-LU / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 9.4 mg/mL, 3:3 Enzyme:Well, 100 mM HEPES pH 7.5, 8% Ethylene glycol, 7% Polyethylene glycol 8000, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→58.46 Å / Num. obs: 28737 / % possible obs: 78.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.051 / Rsym value: 0.057 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.7 / % possible all: 12 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B94 Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.624 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.21
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.437 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|