SAXSdb — 6p7e

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed DNA polymerase

Enterobacteria phage T7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–704	Mutation：D5A, E7A	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248
2	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain B； UniProt 1–704	Mutation：D5A, E7A	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248
3	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain C； UniProt 1–704	Mutation：D5A, E7A	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 THR-ASP-PHE peptide × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248
4	Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain D； UniProt 1–704	Mutation：D5A, E7A	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6P7E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SKR T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 3 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 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 Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5	Resolution 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 Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5	Resolution 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 Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 1 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 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 Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 1 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 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 Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5	Resolution 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 Deposited 2004-03-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	MG MAGNESIUM ION × 3 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；VAPOR DIFFUSION, HANGING DROP, pH 7.5	Resolution 2.30 Å R-free 0.279
1T7P T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN Deposited 1997-09-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：DEL(118-123)	DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.279
1T8E T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. Deposited 2004-05-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Not recorded	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 provides none of the parsed conditions	Resolution 2.54 Å R-free 0.255
1TK0 T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site Deposited 2004-06-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG8000, Amonium Sulfate, PEG400, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.30 Å R-free 0.263
1TK5 T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand Deposited 2004-06-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；PEG 8000, Ammonium Sulfate. PEG400, Etylen Glyco, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.20 Å R-free 0.246
1TK8 T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site Deposited 2004-06-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Not recorded	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 crystallization conditions 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	Resolution 2.50 Å R-free 0.261
1TKD T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site Deposited 2004-06-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Not recorded	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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；PEG8000, Ammonium Sulfate, PEG400, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.49 Å R-free 0.265
1X9M T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA Deposited 2004-08-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：deletion of 118-123	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；PEG 8000, ammonium sulfate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 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. Deposited 2004-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：deletion of 118-123	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 8000, ammonium sulfate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 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. Deposited 2004-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：deletion of 118-123	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 8000, ammonium sulfate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.258
1ZYQ T7 DNA polymerase in complex with 8oG and incoming ddATP Deposited 2005-06-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：K536A	MG MAGNESIUM ION × 3 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG, amonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.272
2AJQ Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing Deposited 2005-08-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–704（704 aa）	Mutation：Residues 5 and 7 mutated to Ala	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.60 Å R-free 0.284
2AJQ Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing Deposited 2005-08-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain F 1–704（704 aa）	Mutation：Residues 5 and 7 mutated to Ala	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.60 Å R-free 0.284
5IKN Crystal Structure of the T7 Replisome in the Absence of DNA Deposited 2016-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–704（704 aa） Chain B 1–704（704 aa） Chain C 1–704（704 aa）	Mutation：D5A, E7A Mutation：D5A, E7A Mutation：D5A, E7A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；1.47-1.62M Sodium Formate 0.1M Tris pH 7.5	Resolution 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) Deposited 2018-11-28	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain H 1–704（704 aa）	Mutation：D5A, E7A	MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 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) Deposited 2018-12-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric	Chain H 1–704（704 aa）	Mutation：D5A, E7A	ZN ZINC ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 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) Deposited 2018-12-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: nonameric	Chain H 1–704（704 aa）	Mutation：D5A, E7A	TTP THYMIDINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 7 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 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) Deposited 2018-12-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: nonameric	Chain H 1–704（704 aa）	Mutation：D5A, E7A	ZN ZINC ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 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) Deposited 2018-12-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: nonameric	Chain H 1–704（704 aa）	Mutation：D5A, E7A	ZN ZINC ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

23 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPOL_BPT7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–704； UniProt 1–704 Author chain B； PDBConstruct 1–704； UniProt 1–704 Author chain C； PDBConstruct 1–704； UniProt 1–704 Author chain D； PDBConstruct 1–704； UniProt 1–704

TrxA

Escherichia coli

UniProt Q14F07

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain E； UniProt 36–144	Not recorded	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248
2	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain F； UniProt 36–144	Not recorded	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248
3	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain G； UniProt 36–144	Not recorded	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 THR-ASP-PHE peptide × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248
4	Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain H； UniProt 36–144	Not recorded	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGPA)-3') ; × 1 DNA (25-MER) × 1 TTP* THYMIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；25% PEG 4000, 0.1M LiSO4, and 0.1 M Tris pH 7.5	Resolution 3.00 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6P7E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GDG Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer Deposited 2018-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 37–144（108 aa） Fragment：UNP residues 37-144,UNP residues 8-316	Not recorded	NEC N-ETHYL-5'-CARBOXAMIDO ADENOSINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.11 Å
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) Deposited 2018-11-28	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain I 36–144（109 aa）	Not recorded	MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q14F07_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–109； UniProt 36–144 Author chain F； PDBConstruct 1–109； UniProt 36–144 Author chain G； PDBConstruct 1–109； UniProt 36–144 Author chain H； PDBConstruct 1–109； UniProt 36–144

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6p7e
Deposition date deposition_date	2019-06-05
Structure title title	Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase
Keywords keywords	DNA Replication, DNA polymerase, DNA binding protein, TRANSFERASE-DNA BINDING PROTEIN-DNA complex; TRANSFERASE/DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	58.30 Å
Radius of gyration Rg (electron density) rg_electron	58.22 Å
Forward intensity I(0) i0	2887990000.00
Molecular weight molecular_weight	412320.0 kDa
Excluded volume excluded_volume	499100 Å³
Envelope volume envelope_volume	786420 Å³
Hydration-shell volume shell_volume	110930 Å³
Envelope diameter envelope_diameter	208.2 Å
Shell Rg shell_rg	61.87 Å
Envelope Rg envelope_rg	57.03 Å
Shape Rg shape_rg	58.20 Å
Total Rg total_rg	58.34 Å
Total atoms total_atoms	28800
Residues n_residues	3317
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	197.6 Å
Rg (real space) rg_real	58.19 Å
Rg uncertainty (real space) rg_real_error	1.97 Å
I(0) (real space) i0_real	2.8880e+09
I(0) uncertainty (real space) i0_real_error	6.3440e+07
Rg (reciprocal space) rg_reciprocal	58.38 Å
I(0) (reciprocal space) i0_reciprocal	2889000000.0000
Solution quality estimate total_estimate	0.8748
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	73.2 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.330
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	135300000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.844

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	DNA-directed DNA polymerase
Molecular weight formula_weight	79703.6 kDa
EC 编号 ec_number	2.7.7.7,3.1.11.-
Mutation mutation	D5A, E7A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	28831

MIVSAIAANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH

来源 Source

来源生物 organism	Enterobacteria phage T7
通用名 common_name	Bacteriophage T7
NCBI Class编号 ncbi_taxonomy_id	10760
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	TrxA
Molecular weight formula_weight	11818.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ;
Molecular weight formula_weight	6551.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,K,M,O

GGCAGGTGGTCTTGCCGGTGA

Entity 4 Entity 4 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7518.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,L,N,P

CCCATCACCGGCAAGACCACCTGCC

Entity 5 Entity 5 polymer

Description description	ASP-THR-ASP-PHE peptide
Molecular weight formula_weight	496.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V

DTDF

Entity 6 Entity 6 polymer

Description description	THR-ASP-PHE peptide
Molecular weight formula_weight	381.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

TDF

Entity 7 Entity 7 non-polymer

Description description	THYMIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	482.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	6p7eA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1060 — Taq DNA Polymerase; Chain T, domain 4
Homologous superfamily homologous superfamily	10 — Taq DNA Polymerase; Chain T, domain 4

Domain ID domain_id	6p7eB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6p7eF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6p7eG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6p7eH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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8. Citations (1)

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Unit-cell length a length_a	100.724 Å
Unit-cell length b length_b	102.698 Å
Unit-cell length c length_c	148.885 Å
Unit-cell angle α angle_alpha	91.36 °
Unit-cell angle β angle_beta	96.83 °
Unit-cell angle γ angle_gamma	113.11 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.001 Å
Low-resolution limit resolution_low	49.129 Å
R factor r_factor	0.2159
R_work r_work	0.2142
R_free r_free	0.2481

fit	/app/data/saxs_computation/p7/6p7e/6p7e.fit
pddf	/app/data/pr_computation/p7/6p7e/6p7e.pr.out
profile	/app/data/saxs_computation/p7/6p7e/6p7e.dat

Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed DNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

TrxA

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)