+Open data
-Basic information
Entry | Database: PDB / ID: 2voa | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of an AP Endonuclease from Archaeoglobus fulgidus | ||||||
Components |
| ||||||
Keywords | LYASE / EXOIII / AP ENDONUCLEASE / ARCHAEOGLOBUS FULGIDUS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kuettner, E.B. / Schmiedel, R. / Greiner-Stoffele, T. / Strater, N. | ||||||
Citation | Journal: DNA Repair / Year: 2009 Title: Structure and Function of the Abasic Site Specificity Pocket of an Ap Endonuclease from Archaeoglobus Fulgidus. Authors: Schmiedel, R. / Kuettner, E.B. / Keim, A. / Strater, N. / Greiner-Stoffele, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and Preliminary X-Ray Characterization of Two Thermostable DNA Nucleases Authors: Kuettner, E.B. / Pfeifer, S. / Keim, A. / Greiner-Stoffele, T. / Strater, N. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2voa.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2voa.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 2voa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2voa_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2voa_full_validation.pdf.gz | 481 KB | Display | |
Data in XML | 2voa_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2voa_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2voa ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2voa | HTTPS FTP |
-Related structure data
Related structure data | 1akoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29810.215 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: DSM4304 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B(DE3)-RIL References: UniProt: O29675, DNA-(apurinic or apyrimidinic site) lyase #2: DNA chain | | Mass: 3086.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | V217G | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.67 % / Description: NONE |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: HANGING-DROP METHOD AT 292 K WITH 1 MICROLITER OF RESERVOIR AND PROTEIN SOLUTION EACH. TRIS-HCL PH 8.5. PROTEIN: 17 MG/ML AF_EXO, 0.53 MM DS-DNA, 9 MM MES-NAOH PH 6, 0.28 M NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9537 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 10, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 64871 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AKO Resolution: 1.7→29.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.57 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED 5'-END PHOSPHATES OF DNA WERE NOT MODELED. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.56 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|