+Open data
-Basic information
Entry | Database: PDB / ID: 4uob | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Deinococcus radiodurans Endonuclease III-3 | ||||||
Components | ENDONUCLEASE III-3 | ||||||
Keywords | LYASE / ENDONUCLEASE III / FES CLUSTER / BASE EXCISION REPAIR / DNA GLYCOSYLASE / DEINOCOCCUS RADIODURANS | ||||||
Function / homology | Function and homology information base-excision repair / 4 iron, 4 sulfur cluster binding / endonuclease activity / metal ion binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å | ||||||
Authors | Sarre, A. / Okvist, M. / Klar, T. / Hall, D. / Smalas, A.O. / McSweeney, S. / Timmins, J. / Moe, E. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Structural and Functional Characterization of Two Unusual Endonuclease III Enzymes from Deinococcus Radiodurans. Authors: Sarre, A. / Okvist, M. / Klar, T. / Hall, D.R. / Smalas, A.O. / Mcsweeney, S. / Timmins, J. / Moe, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uob.cif.gz | 158.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uob.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uob ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uob | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31480.668 Da / Num. of mol.: 1 / Fragment: RESIDUES 76-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q9RVU4, DNA-(apurinic or apyrimidinic site) lyase |
---|
-Non-polymers , 5 types, 450 molecules
#2: Chemical | ChemComp-SF4 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-CO / | ||||
#4: Chemical | #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | OUR CLONE IS N-TERMINALLY TRUNCATED - WE DELETED THE FIRST 75 AMINO ACIDS AND ADDED AN N-TERMINAL ...OUR CLONE IS N-TERMINALLY |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 44.5 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.1M MES PH6.5, 1.4M AMMONIUM SULPHATE AND 0.01M COBALT (II) CHLORIDE HEXAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07812, 1.735 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.31→50 Å / Num. obs: 61009 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4 | |||||||||
Reflection shell | Resolution: 1.31→1.34 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 90.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.31→41.932 Å / SU ML: 0.11 / σ(F): 1.99 / Phase error: 14.7 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→41.932 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|