- PDB-4ba9: The structural basis for the coordination of Y-family Translesion... -
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基本情報
登録情報
データベース: PDB / ID: 4ba9
タイトル
The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
要素
DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
キーワード
TRANSFERASE / TLS / DNA REPAIR
機能・相同性
機能・相同性情報
deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis ...deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding 類似検索 - 分子機能
DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / Rad18-like CCHC zinc finger / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / DNA repair protein Rev1 / DNA polymerase type-Y, HhH motif ...DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / Rad18-like CCHC zinc finger / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / DNA repair protein Rev1 / DNA polymerase type-Y, HhH motif / IMS family HHH motif / : / DNA polymerase IV / DNApol eta/Rev1, HhH motif / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / BRCA1 C Terminus (BRCT) domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
NICKEL (II) ION / DNA polymerase kappa / DNA repair protein REV1 類似検索 - 構成要素
A: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 B: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 C: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 D: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 ヘテロ分子
A: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 B: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 C: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 D: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 ヘテロ分子
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.9919 Å / 相対比: 1
反射
解像度: 2.73→84.08 Å / Num. obs: 24571 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / 冗長度: 3.7 % / Biso Wilson estimate: 74.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
反射 シェル
解像度: 2.73→2.8 Å / 冗長度: 3.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 99.9
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解析
ソフトウェア
名称
バージョン
分類
XDS
データ削減
SCALA
データスケーリング
SHELX
位相決定
SHARP
位相決定
BUSTER
2.10.0
精密化
精密化
構造決定の手法: 単波長異常分散 開始モデル: NONE 解像度: 2.73→42.82 Å / Cor.coef. Fo:Fc: 0.9222 / Cor.coef. Fo:Fc free: 0.8926 / SU R Cruickshank DPI: 0.74 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.804 / SU Rfree Blow DPI: 0.316 / SU Rfree Cruickshank DPI: 0.317 詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5295. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5295. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=18.