SAXSdb — 5ikn

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	DNA primase/helicase × 7 （P03692） Thioredoxin-1 × 3 （P0AA27）	Consistent with protein count

Other States of the Same Protein in the Database

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

DNA primase/helicase

Enterobacteria phage T7

UniProt P03692

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	DNA-directed DNA polymerase × 3 （P00581） Thioredoxin-1 × 3 （P0AA27）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIM_BPT7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–486； UniProt 64–549 Author chain E； PDBConstruct 1–486； UniProt 64–549 Author chain F； PDBConstruct 1–486； UniProt 64–549 Author chain G； PDBConstruct 1–486； UniProt 64–549 Author chain H； PDBConstruct 1–486； UniProt 64–549 Author chain I； PDBConstruct 1–486； UniProt 64–549 Author chain J； PDBConstruct 1–486； UniProt 64–549

Thioredoxin-1

Escherichia coli O157:H7

UniProt P0AA27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	DNA-directed DNA polymerase × 3 （P00581） DNA primase/helicase × 7 （P03692）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIO_ECO57
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 1–105； UniProt 4–108 Author chain L； PDBConstruct 1–105； UniProt 4–108 Author chain M； PDBConstruct 1–105； UniProt 4–108

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	5ikn
Deposition date deposition_date	2016-03-03
Structure title title	Crystal Structure of the T7 Replisome in the Absence of DNA
Keywords keywords	Replisome, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5ikn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ikn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ikn__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	70.71 Å
Rg (electron density)	71.19 Å
Total Rg	70.97 Å
Atom count	43846
Residues	5604
Excluded volume	777810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ikn__assembly_1__model_1`	tridecameric （13）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	43846

MIVSAIAANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH

Source Source

Source organism organism	Enterobacteria phage T7
NCBI taxonomy ID ncbi_taxonomy_id	10760
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA primase/helicase
Molecular weight formula_weight	53815.0 kDa
EC 编号 ec_number	2.7.7.-,3.6.4.12
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

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

MTYNVWNFGESNGRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANECHLNGHDREIMEQVWNAGPWIPDGVVSALSLRERIREHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLVRILKCRFTGDTGIAGYMEYNKETGWLEPSSYSG

Source Source

Source organism organism	Enterobacteria phage T7
NCBI taxonomy ID ncbi_taxonomy_id	10760
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Thioredoxin-1
Molecular weight formula_weight	11414.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,L,M

KIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	174.866 Å
Unit-cell length b length_b	238.091 Å
Unit-cell length c length_c	243.466 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	28

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	4.802 Å
Low-resolution limit resolution_low	29.983 Å
R factor r_factor	0.2768
R_work r_work	0.2747
R_free r_free	0.3178

Crystal Structure of the T7 Replisome in the Absence of DNA

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

DNA primase/helicase

State in the Current Structure

Other States of the Same Protein in the Database

Thioredoxin-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ikn__assembly_1__model_1

5ikn__assembly_1__model_1 | I(q)

5ikn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal Structure of the T7 Replisome in the Absence of DNA

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA primase/helicase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Thioredoxin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ikn__assembly_1__model_1

5ikn__assembly_1__model_1 | I(q)

5ikn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)