+Open data
-Basic information
Entry | Database: PDB / ID: 1b43 | ||||||
---|---|---|---|---|---|---|---|
Title | FEN-1 FROM P. FURIOSUS | ||||||
Components | PROTEIN (FEN-1) | ||||||
Keywords | TRANSFERASE / NUCLEASE / DNA REPAIR / DNA REPLICATION | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / RNA-DNA hybrid ribonuclease activity / manganese ion binding / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å | ||||||
Authors | Hosfield, D.J. / Mol, C.D. / Shen, B. / Tainer, J.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Authors: Hosfield, D.J. / Mol, C.D. / Shen, B. / Tainer, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1b43.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1b43.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 1b43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b43_validation.pdf.gz | 372 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1b43_full_validation.pdf.gz | 386.9 KB | Display | |
Data in XML | 1b43_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1b43_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b43 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b43 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.1574, -0.9873, -0.0205), Vector: |
-Components
#1: Protein | Mass: 38798.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUE 1 IN THE STRUCTURE IS THE FIRST ORDERED RESIDUE, WHICH CORRESPONDS TO GLY2 IN THE SEQUENCE. Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET15-B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O93634 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: 60 % AMMONIUM SULFATE 100 MM IMIDAZOLE MALATE 50 MM MGCL2, pH 6.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and precipitant solutions | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 62063 / % possible obs: 96 % / Redundancy: 3.4 % / Biso Wilson estimate: 62.3 Å2 / Rsym value: 0.038 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.346 / % possible all: 88.3 |
Reflection | *PLUS Num. measured all: 208396 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 88.3 % / Rmerge(I) obs: 0.346 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PAR |