[English] 日本語
Yorodumi- PDB-1em8: Crystal structure of chi and psi subunit heterodimer from DNA POL III -
+Open data
-Basic information
Entry | Database: PDB / ID: 1em8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of chi and psi subunit heterodimer from DNA POL III | ||||||
Components |
| ||||||
Keywords | GENE REGULATION / DNA Pol III / heterodimer / clamp-loader / alpha-beta fold | ||||||
Function / homology | Function and homology information positive regulation of DNA-templated DNA replication initiation / DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / 3'-5' exonuclease activity / response to radiation / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Gulbis, J.M. / Finkelstein, J. / O'Donnell, M. / Kuriyan, J. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2004 Title: Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex. Authors: Gulbis, J.M. / Kazmirski, S.L. / Finkelstein, J. / Kelman, Z. / O'Donnell, M. / Kuriyan, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1em8.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1em8.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 1em8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1em8_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1em8_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 1em8_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1em8_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1em8 ftp://data.pdbj.org/pub/pdb/validation_reports/em/1em8 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | One biological assembly is a heterodimer constructed from chain A and chain B / One biological assembly is a heterodimer constructed from chain C and chain D |
-Components
#1: Protein | Mass: 16653.742 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28905, DNA-directed DNA polymerase #2: Protein | Mass: 12203.835 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-137 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28632, DNA-directed DNA polymerase #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: methylpentanediol, HEPES, PEG 4000, Glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 K / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 223463 / Num. obs: 218771 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 1 % / Rmerge(I) obs: 0.194 / Num. unique all: 4047 / % possible all: 95.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 32326 / Num. measured all: 218771 |
Reflection shell | *PLUS % possible obs: 95.2 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|