[English] 日本語

- PDB-5ftc: Crystal structure of Pif1 helicase from Bacteroides in complex wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ftc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Pif1 helicase from Bacteroides in complex with ADP | ||||||
![]() | TPR DOMAIN PROTEIN | ||||||
![]() | HYDROLASE / SF1B / G QUADRUPLEX / SH3 DOMAIN / CONFORMATIONAL CHANGE | ||||||
Function / homology | ![]() DNA helicase activity / telomere maintenance / DNA repair / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, W.-F. / Dai, Y.-X. / Duan, X.-L. / Liu, N.-N. / Shi, W. / Li, M. / Dou, S.-X. / Li, N. / Dong, Y.-H. / Rety, S. / Xi, X.-G. | ||||||
![]() | ![]() Title: Crystal Structures of the Bspif1 Helicase Reveal that a Major Movement of the 2B SH3 Domain is Required for DNA Unwinding Authors: Chen, W.-F. / Dai, Y.-X. / Duan, X.-L. / Liu, N.-N. / Shi, W. / Li, N. / Li, M. / Dou, S.-X. / Dong, Y.-H. / Rety, S. / Xi, X.-G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 192.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 153.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5ftbSC ![]() 5ftdC ![]() 5fteC ![]() 5ftfC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 49730.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ADP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | NCBI REFERENCE SEQUENCE WP_008647876.1 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.1M BIS-TRIS PROPANE PH 6.5 0.1 CALCIUM ACETATE 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 77 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→75.21 Å / Num. obs: 25850 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Biso Wilson estimate: 50.21 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.56 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.82 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5FTB Resolution: 2.269→57.208 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 29.75 / 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: 2.269→57.208 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|