+Open data
-Basic information
Entry | Database: PDB / ID: 7rcg | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | I-OnuI_e-hPD1-f final stage reengineered variant of I-OnuI | ||||||||||||
Components |
| ||||||||||||
Keywords | DNA BINDING PROTEIN/DNA / meganuclease / gene editing / protein engineering / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||||||||
Biological species | Synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.368 Å | ||||||||||||
Authors | Smiley, A.T. / Werther, R.A. / Stoddard, B.L. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: To Be Published Title: Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease Authors: Werther, R.A. / Ubilla-Rodriguez, N.C. / Smiley, A.T. / Havens, K. / Lambert, A.R. / Stoddard, B.L. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rcg.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rcg.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rcg_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7rcg_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 7rcg_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 7rcg_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/7rcg ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rcg | HTTPS FTP |
-Related structure data
Related structure data | 7rccC 7rcdC 7rceC 7rcfC 3qqyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34940.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 8064.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 7917.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
-Non-polymers , 4 types, 67 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|---|
Sequence details | The wild type homing endonuclease was extensively engineered to generate I-OnuI_e-hPD1-f. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.26 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 200mM ammonium sulfate, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 108 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 23, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.368→50 Å / Num. obs: 19975 / % possible obs: 97.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.033 / Rrim(I) all: 0.076 / Χ2: 0.991 / Net I/σ(I): 11.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QQY Resolution: 2.368→27.952 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.68 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.57 Å2 / Biso mean: 32.8825 Å2 / Biso min: 13.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.368→27.952 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|