[English] 日本語
Yorodumi- PDB-5omv: Ternary complex of 9N DNA polymerase in the replicative state wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5omv | ||||||
---|---|---|---|---|---|---|---|
Title | Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / ternary complex / DNA polymerase / triphosphate | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Thermococcus sp. 9oN-7 (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å | ||||||
Authors | Betz, K. / Marx, A. / Diederichs, K. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Crystal structures of ternary complexes of archaeal B-family DNA polymerases. Authors: Kropp, H.M. / Betz, K. / Wirth, J. / Diederichs, K. / Marx, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5omv.cif.gz | 365.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5omv.ent.gz | 291.8 KB | Display | PDB format |
PDBx/mmJSON format | 5omv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5omv_validation.pdf.gz | 823.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5omv_full_validation.pdf.gz | 835.8 KB | Display | |
Data in XML | 5omv_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 5omv_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5omv ftp://data.pdbj.org/pub/pdb/validation_reports/om/5omv | HTTPS FTP |
-Related structure data
Related structure data | 5omfC 5omqC 4k8xS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/480 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 89826.570 Da / Num. of mol.: 1 / Mutation: D141A, E143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus sp. 9oN-7 (archaea) / Gene: pol, polA / Production host: Escherichia coli (E. coli) / References: UniProt: Q56366, DNA-directed DNA polymerase |
---|
-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 186 molecules
#4: Chemical | ChemComp-MN / | ||||||
---|---|---|---|---|---|---|---|
#5: Chemical | ChemComp-GOL / | ||||||
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-DTP / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium acetate trihydrate pH 4.5, 6% isopropanol, 36% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999973488495 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999973488495 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.482 Å / Num. obs: 130652 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rrim(I) all: 0.142 / Net I/σ(I): 7.88 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.37 / Num. unique obs: 21057 / Rrim(I) all: 3.603 / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K8X Resolution: 2.003→47.482 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 30.83
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.003→47.482 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|