SAXSdb — 1d8y

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

DNA POLYMERASE I

Escherichia coli

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 Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 324–928	Fragment：KLENOW FRAGMENT Mutation：D355A, E357A	D(T)19 OLIGOMER × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；SODIUM CITRATE, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.08 Å R-free 0.233

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 1D8Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DPI STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP Deposited 1987-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 324–928（605 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1KFD CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE Deposited 1993-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 324–928（605 aa）	Not recorded	CTP CYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.90 Å
1KFS DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX Deposited 1997-08-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 324–928（605 aa）	Mutation：V324M	MG MAGNESIUM ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；1.4 M NA CITRATE PH 5.8	Resolution 2.10 Å R-free 0.219
1KLN DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX Deposited 1994-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 324–928（605 aa）	Mutation：D355A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；290 K；pH 6.80, VAPOR DIFFUSION, temperature 290.00K	Resolution 3.20 Å
1KRP DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex Deposited 1997-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 324–928（605 aa）	Mutation：V324M	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；1.4 M NA CITRATE PH 5.8	Resolution 2.20 Å R-free 0.255
1KSP DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex Deposited 1997-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 324–928（605 aa）	Mutation：V324M	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；1.4 M NA CITRATE PH 5.8	Resolution 2.30 Å R-free 0.241
1QSL KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION Deposited 1999-06-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 324–928（605 aa） Fragment：KLENOW FRAGMENT	Mutation：V324M	EU EUROPIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；1.5 M SODIUM CITRATE AT 290 K, pH 5.60, VAPOR DIFFUSION, HANGING DROP	Resolution 2.20 Å R-free 0.255
2KFN KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND MANGANESE Deposited 1998-07-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 325–928（604 aa） Fragment：LARGE FRAGMENT, KLENOW FRAGMENT	Mutation：V324M	MN MANGANESE (II) ION × 1 ZN ZINC ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；1.4 M NA CITRATE PH 5.8	Resolution 2.03 Å R-free 0.250
2KFZ KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND ZINC ONLY Deposited 1998-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 325–928（604 aa） Fragment：LARGE FRAGMENT, KLENOW FRAGMENT	Mutation：V324M	ZN ZINC ION × 4 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；1.4 M NA CITRATE PH 5.8	Resolution 2.03 Å R-free 0.255
2KZM KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE Deposited 1998-07-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 324–928（605 aa） Fragment：KLENOW FRAGMENT, LARGE FRAGMENT	Not recorded	MN MANGANESE (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；1.4 M SODIUM CITRATE PH 5.8, pH 5.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.243
2KZZ KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY Deposited 1998-07-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 324–928（605 aa） Fragment：KLENOW FRAGMENT, LARGE FRAGMENT	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；1.4 M SODIUM CITRATE PH 5.8, pH 5.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.25 Å R-free 0.251
8OO6 Pol I bound to extended and displaced DNA section - closed conformation Deposited 2023-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 328–928（601 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8OOY Pol I bound to extended and displaced DNA section - open conformation Deposited 2023-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 328–928（601 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPO1_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–605； UniProt 324–928

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	1d8y
Deposition date deposition_date	1999-10-26
Structure title title	CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA
Keywords keywords	DNA POLYMERASE I, POLY-D(T), TRANSFERASE-DNA COMPLEX; TRANSFERASE/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	27.93 Å
Radius of gyration Rg (electron density) rg_electron	27.32 Å
Forward intensity I(0) i0	77591800.00
Molecular weight molecular_weight	68630.0 kDa
Excluded volume excluded_volume	85736 Å³
Envelope volume envelope_volume	107530 Å³
Hydration-shell volume shell_volume	32910 Å³
Envelope diameter envelope_diameter	95.6 Å
Shell Rg shell_rg	34.74 Å
Envelope Rg envelope_rg	27.18 Å
Shape Rg shape_rg	27.33 Å
Total Rg total_rg	28.01 Å
Total atoms total_atoms	4822
Residues n_residues	605
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	89.0 Å
Rg (real space) rg_real	27.85 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	7.7590e+07
I(0) uncertainty (real space) i0_real_error	1.0670e+06
Rg (reciprocal space) rg_reciprocal	27.88 Å
I(0) (reciprocal space) i0_reciprocal	77590000.0000
Solution quality estimate total_estimate	0.8971
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.259
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19470000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.898

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	D(T)19 OLIGOMER
Molecular weight formula_weight	5734.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	5157

TTTTTTTTTTTTTTTTTTT

Entity 2 Entity 2 polymer

Description description	DNA POLYMERASE I
Molecular weight formula_weight	68091.7 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D355A, E357A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MISYDNYVTILDEETLKAWIAKLEKAPVFAFATATDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d8ya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d1d8ya2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

CATH v4.4 (4 domains)

Domain ID domain_id	1d8yA01
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	1d8yA02
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	1d8yA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	1d8yA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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8. Citations (1)

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Unit-cell length a length_a	101.880 Å
Unit-cell length b length_b	101.880 Å
Unit-cell length c length_c	85.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2330

fit	/app/data/saxs_computation/d8/1d8y/1d8y.fit
pddf	/app/data/pr_computation/d8/1d8y/1d8y.pr.out
profile	/app/data/saxs_computation/d8/1d8y/1d8y.dat

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA

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

DNA POLYMERASE I

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)