[English] 日本語
Yorodumi- PDB-4cej: Crystal structure of AddAB-DNA-ADPNP complex at 3 Angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cej | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AddAB-DNA-ADPNP complex at 3 Angstrom resolution | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HELICASE-NUCLEASE / DNA BREAKS / DNA REPAIR / SINGLE-STRANDED / DNA-BINDING PROTEINS / EXODEOXYRIBONUCLEASE V / EXODEOXYRIBONUCLEASES / HOMOLOGOUS RECOMBINATION | ||||||
Function / homology | Function and homology information DNA helicase complex / DNA 3'-5' helicase / recombinational repair / 5'-3' exonuclease activity / 3'-5' DNA helicase activity / 3'-5' exonuclease activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / double-stranded DNA binding ...DNA helicase complex / DNA 3'-5' helicase / recombinational repair / 5'-3' exonuclease activity / 3'-5' DNA helicase activity / 3'-5' exonuclease activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / double-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA recombination / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Krajewski, W.W. / Wilkinson, M. / Fu, X. / Cronin, N.B. / Wigley, D. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites. Authors: Krajewski, W.W. / Fu, X. / Wilkinson, M. / Cronin, N.B. / Dillingham, M.S. / Wigley, D.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cej.cif.gz | 511.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cej.ent.gz | 407 KB | Display | PDB format |
PDBx/mmJSON format | 4cej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cej_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cej_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4cej_validation.xml.gz | 80.1 KB | Display | |
Data in CIF | 4cej_validation.cif.gz | 107.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/4cej ftp://data.pdbj.org/pub/pdb/validation_reports/ce/4cej | HTTPS FTP |
-Related structure data
Related structure data | 4cehC 4ceiC 3u44S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-ATP-DEPENDENT ... , 2 types, 2 molecules AB
#1: Protein | Mass: 141218.844 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) Plasmid: PCOLADUET-1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 (DE3) References: UniProt: P23478, Hydrolases; Acting on ester bonds, DNA helicase |
---|---|
#2: Protein | Mass: 134769.406 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) Plasmid: PCOLADUET-1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 (DE3) References: UniProt: P23477, Hydrolases; Acting on ester bonds, DNA helicase |
-DNA chain , 1 types, 1 molecules X
#3: DNA chain | Mass: 21477.703 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: ANNEALED HAIRPIN DUPLEX WITH UNPAIRED SINGLE-STRANDED 3' AND 5' TAILS Source: (synth.) SYNTHETIC CONSTRUCT (others) |
---|
-Non-polymers , 4 types, 12 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SF4 / | #7: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | MAGNESIUM ION (MG): COORDINATE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.1M TRIS-HCL PH 7.5, 11% PEG 4000, 0.1M MAGNESIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 3→35.55 Å / Num. obs: 57963 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 3→3.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U44 Resolution: 3→29.731 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 28.59 / 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: 3→29.731 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|