当前蛋白身份：P00581
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相关结构差异明细
一行代表一个 PDB 条目中的一个 biological assembly；同一蛋白的多个单体会分别列出。
| PDB 条目 | Assembly / 聚集状态 | 构建体 | 突变与修饰 | 配体、离子与非聚合物 | 实验方法 | 实验环境 | 结构质量 |
|---|---|---|---|---|---|---|---|
| 1SKR T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP 提交 2004-03-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 3 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG 8000, ammonium sulfate, aces, ethylene glycol, DTT , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
分辨率 2.40 Å R-free 0.270 |
| 1SKS Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template 提交 2004-03-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5
|
分辨率 2.30 Å R-free 0.266 |
| 1SKW Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template 提交 2004-03-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5
|
分辨率 2.30 Å R-free 0.278 |
| 1SL0 Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide 提交 2004-03-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 1 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP
|
分辨率 3.20 Å R-free 0.351 |
| 1SL0 Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide 提交 2004-03-05 | Assembly 2 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 C
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 1 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP
|
分辨率 3.20 Å R-free 0.351 |
| 1SL1 Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template 提交 2004-03-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5
|
分辨率 2.20 Å R-free 0.262 |
| 1SL2 Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide 提交 2004-03-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | MG MAGNESIUM ION × 3 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5
|
分辨率 2.30 Å R-free 0.279 |
| 1T7P T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN 提交 1997-09-24 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：DEL(118-123) | DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 | X-RAY DIFFRACTION |
X-ray结晶条件
pH 6.5；pH 6.5
|
分辨率 2.20 Å R-free 0.279 |
| 1T8E T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. 提交 2004-05-12 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
未记录 | MG MAGNESIUM ION × 3 SO4 SULFATE ION × 1 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION | mmCIF 未提供已读取条件 | 分辨率 2.54 Å R-free 0.255 |
| 1TK0 T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site 提交 2004-06-07 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：deletion 118-123 | MG MAGNESIUM ION × 3 SO4 SULFATE ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 1PE PENTAETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG8000, Amonium Sulfate, PEG400, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
|
分辨率 2.30 Å R-free 0.263 |
| 1TK5 T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand 提交 2004-06-08 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
未记录 | MG MAGNESIUM ION × 1 SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1PE PENTAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；PEG 8000, Ammonium Sulfate. PEG400, Etylen Glyco, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
|
分辨率 2.20 Å R-free 0.246 |
| 1TK8 T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site 提交 2004-06-08 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
未记录 | MG MAGNESIUM ION × 4 SO4 SULFATE ION × 2 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1PE PENTAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG 8000, Ammonium Sulfate, PEG400, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
分辨率 2.50 Å R-free 0.261 |
| 1TKD T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site 提交 2004-06-08 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
未记录 | MG MAGNESIUM ION × 3 SO4 SULFATE ION × 3 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1PE PENTAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG8000, Ammonium Sulfate, PEG400, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
分辨率 2.49 Å R-free 0.265 |
| 1X9M T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA 提交 2004-08-23 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：deletion of 118-123 | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION；pH 7.5；295 K；PEG 8000, ammonium sulfate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, temperature 295K
|
分辨率 2.10 Å R-free 0.236 |
| 1X9S T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide. 提交 2004-08-24 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：deletion of 118-123 | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 8000, ammonium sulfate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
分辨率 2.70 Å R-free 0.279 |
| 1X9W T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide. 提交 2004-08-24 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：deletion of 118-123 | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 8000, ammonium sulfate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
分辨率 2.30 Å R-free 0.258 |
| 1ZYQ T7 DNA polymerase in complex with 8oG and incoming ddATP 提交 2005-06-10 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：K536A | MG MAGNESIUM ION × 3 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG, amonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
分辨率 2.70 Å R-free 0.272 |
| 2AJQ Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing 提交 2005-08-02 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：Residues 5 and 7 mutated to Ala | 未记录非水小分子 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；273 K；A complex of 1x10^-4 M T7 DNA polymerase 5A7A:thioredoxin was assembled
with an equimolar amount of double stranded DNA substrate.
Crystallization
was achieved using a buffer containing 50mM HEPES pH 7.5, 10mM MgCl_2,
2mM DTT, and 0.5 mM terminal ddTTP Seed crystals were grown by hanging
drop vapor diffusion by mixing 1ul each of protein-DNA solution and a
reservoir solutions containing between 16 to 20% PEG 8000, 100mM ACES pH
7.5, 120 ammonium sulfate, 30mM MgCl2, and 5mM DTT. These crystals
were used to streak-seed a grid of protein/reservoir solutions with
concentrations of PEG 8000 between 13 to 15%. Pyramidal crystals
appeared overnight and reached a maximum size of ~150 X 150 X 100 um3
after 3 to 4 days. Crystals were harvested overnight in mother-liquor
containing 10 % PEG 400, temperature 273K, VAPOR DIFFUSION, HANGING DROP
|
分辨率 2.60 Å R-free 0.284 |
| 2AJQ Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing 提交 2005-08-02 | Assembly 2 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 F
1–704（704 aa）
|
突变：Residues 5 and 7 mutated to Ala | 未记录非水小分子 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；273 K；A complex of 1x10^-4 M T7 DNA polymerase 5A7A:thioredoxin was assembled
with an equimolar amount of double stranded DNA substrate.
Crystallization
was achieved using a buffer containing 50mM HEPES pH 7.5, 10mM MgCl_2,
2mM DTT, and 0.5 mM terminal ddTTP Seed crystals were grown by hanging
drop vapor diffusion by mixing 1ul each of protein-DNA solution and a
reservoir solutions containing between 16 to 20% PEG 8000, 100mM ACES pH
7.5, 120 ammonium sulfate, 30mM MgCl2, and 5mM DTT. These crystals
were used to streak-seed a grid of protein/reservoir solutions with
concentrations of PEG 8000 between 13 to 15%. Pyramidal crystals
appeared overnight and reached a maximum size of ~150 X 150 X 100 um3
after 3 to 4 days. Crystals were harvested overnight in mother-liquor
containing 10 % PEG 400, temperature 273K, VAPOR DIFFUSION, HANGING DROP
|
分辨率 2.60 Å R-free 0.284 |
| 5IKN Crystal Structure of the T7 Replisome in the Absence of DNA 提交 2016-03-03 | Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 13 PDB 声明：tridecameric（13） 与蛋白数一致 |
链 A
1–704（704 aa）
链 B
1–704（704 aa）
链 C
1–704（704 aa）
|
突变：D5A, E7A 突变：D5A, E7A 突变：D5A, E7A | 未记录非水小分子 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；295.15 K；1.47-1.62M Sodium Formate
0.1M Tris pH 7.5
|
分辨率 4.80 Å R-free 0.318 |
| 6N7W Structure of bacteriophage T7 leading-strand DNA polymerase (D5A/E7A)/Trx in complex with a DNA fork and incoming dTTP (from multiple lead complexes) 提交 2018-11-28 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 H
1–704（704 aa）
|
突变：D5A, E7A | MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7.5
cryo-EM玻璃化条件
冷冻剂 ETHANE
|
分辨率 4.50 Å |
| 6N9U Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two gp4 subunits bound to an RNA/DNA hybrid and dTTP (from LagS1) 提交 2018-12-04 | Assembly 1 其他组合 异源复合物；蛋白 × 3 PDB 声明：pentameric（5） 与全部聚合物一致 |
链 H
1–704（704 aa）
|
突变：D5A, E7A | ZN ZINC ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7.5
cryo-EM玻璃化条件
冷冻剂 ETHANE
|
分辨率 3.70 Å |
| 6N9V Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1) 提交 2018-12-04 | Assembly 1 其他组合 异源复合物；蛋白 × 7 PDB 声明：nonameric（9） 与全部聚合物一致 |
链 H
1–704（704 aa）
|
突变：D5A, E7A | TTP THYMIDINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 7 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7.5
cryo-EM玻璃化条件
冷冻剂 ETHANE
|
分辨率 4.00 Å |
| 6N9W Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS2) 提交 2018-12-04 | Assembly 1 其他组合 异源复合物；蛋白 × 7 PDB 声明：nonameric（9） 与全部聚合物一致 |
链 H
1–704（704 aa）
|
突变：D5A, E7A | ZN ZINC ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7.5
cryo-EM玻璃化条件
冷冻剂 ETHANE
|
分辨率 4.00 Å |
| 6N9X Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3) 提交 2018-12-04 | Assembly 1 其他组合 异源复合物；蛋白 × 7 PDB 声明：nonameric（9） 与全部聚合物一致 |
链 H
1–704（704 aa）
|
突变：D5A, E7A | ZN ZINC ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 | ELECTRON MICROSCOPY |
cryo-EM缓冲液
pH 7.5
cryo-EM玻璃化条件
冷冻剂 ETHANE
|
分辨率 4.10 Å |
| 6P7E Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase 提交 2019-06-05 | Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric（5） 与全部聚合物一致 |
链 A
1–704（704 aa）
|
突变：D5A, E7A | TTP THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5
|
分辨率 3.00 Å R-free 0.248 |
| 6P7E Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase 提交 2019-06-05 | Assembly 2 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric（5） 与全部聚合物一致 |
链 B
1–704（704 aa）
|
突变：D5A, E7A | TTP THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5
|
分辨率 3.00 Å R-free 0.248 |
| 6P7E Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase 提交 2019-06-05 | Assembly 3 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric（5） 与全部聚合物一致 |
链 C
1–704（704 aa）
|
突变：D5A, E7A | TTP THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5
|
分辨率 3.00 Å R-free 0.248 |
| 6P7E Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase 提交 2019-06-05 | Assembly 4 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric（4） 与全部聚合物一致 |
链 D
1–704（704 aa）
|
突变：D5A, E7A | TTP THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 | X-RAY DIFFRACTION |
X-ray结晶条件
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5
|
分辨率 3.00 Å R-free 0.248 |