[English] 日本語
Yorodumi- PDB-3ory: Crystal structure of Flap endonuclease 1 from hyperthermophilic a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ory | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Flap endonuclease 1 from hyperthermophilic archaeon Desulfurococcus amylolyticus | ||||||
Components | flap endonuclease 1Flap structure-specific endonuclease 1 | ||||||
Keywords | HYDROLASE / endonuclease | ||||||
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 | Desulfurococcus amylolyticus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mase, T. / Kubota, K. / Miyazono, K. / Kawarabayashii, Y. / Tanokura, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus Authors: Mase, T. / Kubota, K. / Miyazono, K. / Kawarabayasi, Y. / Tanokura, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ory.cif.gz | 148.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ory.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ory.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/3ory ftp://data.pdbj.org/pub/pdb/validation_reports/or/3ory | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40879.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfurococcus amylolyticus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z289*PLUS | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN FROM DESULFUROC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 0.1M Tris-HCl, 1.98M ammonium dihydrogen phosphate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2008 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 35852 / % possible obs: 99.8 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2→2.06 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.098 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 38.029 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 23.622 Å / Origin y: 40.091 Å / Origin z: 18.71 Å
|