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- PDB-7sxe: Crystal structure of ligase I with nick duplexes containing cogna... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sxe | ||||||
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Title | Crystal structure of ligase I with nick duplexes containing cognate G:T | ||||||
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![]() | LIGASE/DNA / LIGASE-DNA complex | ||||||
Function / homology | ![]() Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mismatch repair / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA recombination / cell division / intracellular membrane-bounded organelle / DNA repair / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, Q. / Gulkis, M. / McKenna, R. / Caglayan, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair. Authors: Tang, Q. / Gulkis, M. / McKenna, R. / Caglayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.4 KB | Display | ![]() |
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PDB format | ![]() | 232.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sumSC ![]() 7sx5C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74326.656 Da / Num. of mol.: 1 / Fragment: UNP residues 261-918 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 3 types, 3 molecules BCD
#2: DNA chain | Mass: 3405.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 5461.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 38 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-AMP / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 19288 / % possible obs: 99.8 % / Redundancy: 11.4 % / CC1/2: 0.988 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 3→3.05 Å / Num. unique obs: 969 / CC1/2: 0.733 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7SUM Resolution: 3→19.97 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.71 Å2 / Biso mean: 84.9052 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→19.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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