[English] 日本語
![](img/lk-miru.gif)
- PDB-1tez: COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1tez | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | |||||||||
![]() |
| |||||||||
![]() | LYASE/DNA / PHOTOLYASE / DNA REPAIR / LIGHT-DRIVEN ELECTRON TRANSFER / LYASE-DNA COMPLEX | |||||||||
Function / homology | ![]() cellular response to stimulus / deoxyribodipyrimidine photo-lyase / response to stress / deoxyribodipyrimidine photo-lyase activity / nucleobase-containing compound metabolic process / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA repair / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Essen, L.-O. / Carell, T. / Mees, A. / Klar, T. | |||||||||
![]() | ![]() Title: Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair Authors: Mees, A. / Klar, T. / Gnau, P. / Hennecke, U. / Eker, A.P.M. / Carell, T. / Essen, L.-O. #1: ![]() Title: Crystal Structure of DNA Photolyase from Anacystis Authors: Tamada, T. / Kitadokoro, K. / Higuchi, Y. / Inaka, K. / Yasui, A. / De Ruiter, P.E. / Eker, A.P. / Miki, K. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 459.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 368 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 90.1 KB | Display | |
Data in CIF | ![]() | 129.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qnfS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||
3 | ![]()
| ||||||||||||||||||||
4 | ![]()
| ||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
-DNA chain , 4 types, 8 molecules IKJLMONP
#1: DNA chain | Mass: 3259.219 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Formacetal linkage replaces phosphate linkage between T7 and T8 of chains I and K Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 2749.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 1166.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 1505.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-Protein , 1 types, 4 molecules ABCD
#5: Protein | Mass: 53474.418 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SYNTHETIC DNA OLIGONUCLEOTIDES ENGINEERED AS COUNTERSTRAND Source: (gene. exp.) ![]() Species: Synechococcus elongatus / Strain: PCC 6301 / Cellular location: CYTOPLASM / Gene: Synpcc7942_0112 / Plasmid: PET3A / Cellular location (production host): CYTOPLASM / Production host: ![]() ![]() References: UniProt: Q31S25, UniProt: P05327*PLUS, deoxyribodipyrimidine photo-lyase |
---|
-Non-polymers , 4 types, 1624 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/HDF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/HDF.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-FAD / #8: Chemical | ChemComp-HDF / #9: Water | ChemComp-HOH / | |
---|
-Details
Compound details | COMPOUND THE CYCLOBUTANNonpolymer details | HETEROGEN DESOXYTHYM | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.2 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K | ||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 27, 2004 / Details: MIRRORS |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 218105 / Num. obs: 218105 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.1 / % possible all: 81.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QNF Resolution: 1.8→29.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2423887.54 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7551 Å2 / ksol: 0.37764 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|