- PDB-4m0a: Human DNA Polymerase Mu post-catalytic complex -
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基本情報
登録情報
データベース: PDB / ID: 4m0a
タイトル
Human DNA Polymerase Mu post-catalytic complex
要素
DNA-directed DNA/RNA polymerase mu
downstream primer strand
template strand
upstream primer strand
キーワード
TRANSFERASE/DNA / polymerase / DNA break repair / TRANSFERASE-DNA complex
機能・相同性
機能・相同性情報
somatic hypermutation of immunoglobulin genes / B cell differentiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus 類似検索 - 分子機能
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X ...DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
: / PYROPHOSPHATE / DNA / DNA-directed DNA/RNA polymerase mu 類似検索 - 構成要素
DNA-directedDNA/RNApolymerasemu / Pol Mu / Terminal transferase
分子量: 40054.434 Da / 分子数: 1 / 断片: UNP residues 132-494 / 由来タイプ: 組換発現 詳細: Modified version of the pGEX4T3 vector backbone, where a TEV protease cleavage site has been inserted downstream of the thrombin cleavage site, and the sequence of the multicloning site has ...詳細: Modified version of the pGEX4T3 vector backbone, where a TEV protease cleavage site has been inserted downstream of the thrombin cleavage site, and the sequence of the multicloning site has been replaced by that of the pMALX vector (Moon et al, 2010). Three TGA stop codons have been inserted downstream of the multicloning site, each utilizing a different reading frame. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: POLM, polmu / プラスミド: pGEXM / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9NP87, DNA-directed DNA polymerase
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DNA鎖 , 3種, 3分子 TPD
#2: DNA鎖
templatestrand
分子量: 2740.812 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: synthesized by Oligos Etc
#3: DNA鎖
upstreamprimerstrand
分子量: 1495.023 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: synthesized by Oligos Etc
#4: DNA鎖
downstreamprimerstrand
分子量: 1191.818 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: synthesized by Oligos Etc
温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: Crystals were grown by mixing 1uL protein/DNA mixture with 1uL mother liquor (85-90mM HEPES pH 7.5, 17-18% PEG4000), using the sitting drop vapor diffusion technique. Crystals were ...詳細: Crystals were grown by mixing 1uL protein/DNA mixture with 1uL mother liquor (85-90mM HEPES pH 7.5, 17-18% PEG4000), using the sitting drop vapor diffusion technique. Crystals were transferred in two steps to a cryoprotectant solution containing 0.1M HEPES pH 7.5, 10mM MgCl2, 50mM NaCl, 20% PEG4000, 5% glycerol, 15% ethylene glycol, 10mM dTTP for 16 hours. The crystals were then backsoaked in cryoprotectant containing 2mM pyrophosphate. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
構造決定の手法: 分子置換 開始モデル: Ternary complex of human Polymerase Mu 解像度: 1.85→31.381 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8756 / SU ML: 0.19 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 19.05 / 立体化学のターゲット値: ML
Rfactor
反射数
%反射
Selection details
Rfree
0.2003
1945
4.99 %
random
Rwork
0.1626
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obs
0.1645
38959
98.15 %
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all
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39012
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溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL