[English] 日本語
Yorodumi- PDB-4xrh: Human DNA polymerase lambda- MgdTTP binary and complex with 6 pai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xrh | ||||||
---|---|---|---|---|---|---|---|
Title | Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/DNA / DNA polymerase lambda / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / Nonhomologous End-Joining (NHEJ) / nucleotide-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / Nonhomologous End-Joining (NHEJ) / nucleotide-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Liu, M.S. / Tsai, M.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda Authors: Liu, M.S. / Tsai, H.Y. / Liu, X.X. / Ho, M.C. / Wu, W.J. / Tsai, M.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xrh.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xrh.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 4xrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xrh_validation.pdf.gz | 761 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xrh_full_validation.pdf.gz | 768.8 KB | Display | |
Data in XML | 4xrh_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4xrh_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/4xrh ftp://data.pdbj.org/pub/pdb/validation_reports/xr/4xrh | HTTPS FTP |
-Related structure data
Related structure data | 4xq8C 5ca7C 5cb1C 5chgC 5cj7C 5cp2C 5cr0C 5cwrC 5ddmC 5ddyC 5dkwC 1xslS 4w5d S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 37479.750 Da / Num. of mol.: 2 / Fragment: UNP residues 242-575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGP5, DNA-directed DNA polymerase |
---|
-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-MG / |
---|---|
#5: Chemical | ChemComp-TTP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→30 Å / Num. obs: 17723 / % possible obs: 99.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.153 / Χ2: 1 / Net I/av σ(I): 11.261 / Net I/σ(I): 5.8 / Num. measured all: 98387 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Χ2: 1 / Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XSL Resolution: 3→29.375 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.62 / 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→29.375 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|