+Open data
-Basic information
Entry | Database: PDB / ID: 4wa8 | ||||||
---|---|---|---|---|---|---|---|
Title | Methanopyrus Kandleri FEN-1 nuclease | ||||||
Components | Flap endonuclease 1 | ||||||
Keywords | HYDROLASE / DNA nuclease / Nucleotide excision repair | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | Methanopyrus kandleri (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shah, S. / Dunten, P. / Horton, N.C. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: Structure and specificity of FEN-1 from Methanopyrus kandleri. Authors: Shah, S. / Dunten, P. / Stiteler, A. / Park, C.K. / Horton, N.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wa8.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wa8.ent.gz | 202.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wa8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wa8_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wa8_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 4wa8_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4wa8_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/4wa8 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/4wa8 | HTTPS FTP |
-Related structure data
Related structure data | 1rxwS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 339 / Label seq-ID: 8 - 346
|
-Components
#1: Protein | Mass: 41018.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanopyrus kandleri (archaea) / Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938 / Gene: fen, MK0566 / Plasmid: pMAL_c4X / Production host: Escherichia coli (E. coli) References: UniProt: Q8TXU4, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.66 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, Tris-HCL, sodium chloride, calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→74.43 Å / Num. obs: 35363 / % possible obs: 96.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.2 / % possible all: 88.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RXW Resolution: 2.2→74.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.732 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.506 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→74.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|