SAXSdb — 1cw0

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

PROTEIN (DNA MISMATCH ENDONUCLEASE)

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(APCPGPTPAPCPCPTPGPGPCPT)-3') ; × 1 ;DNA (5'-D(APGPC)-3') ; × 1 ;DNA (5'-D(PTPAPGPGPTPAPCPGPT)-3') ; × 1 MAGNESIUM ION × 2 ZINC ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VSR_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–155； UniProt 1–155

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	1cw0
Deposition date deposition_date	1999-08-25
Structure title title	CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA
Keywords keywords	PROTEIN-DNA COMPLEX, MISMATCH, INTERCALATION, ZINC, HYDROLASE/DNA, HYDROLASE-DNA complex; HYDROLASE/DNA
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.

1cw0__assembly_1__model_1

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

Download this curve (.dat)

1cw0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1cw0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.21 Å
Rg (electron density)	17.30 Å
Total Rg	18.12 Å
Atom count	1751
Residues	179
Excluded volume	29445 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1cw0__assembly_1__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APCPGPTPAPCPCPTPGPGPCPT)-3') ;
Molecular weight formula_weight	3638.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M
Atom count atom_count	1957

ACGTACCTGGCT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APGP*C)-3') ;
Molecular weight formula_weight	886.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

AGC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PTPAPGPGPTPAPCPGP*T)-3') ;
Molecular weight formula_weight	2770.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	O

TAGGTACGT

Entity 4 Entity 4 polymer

Description description	PROTEIN (DNA MISMATCH ENDONUCLEASE)
Molecular weight formula_weight	17914.5 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cw0a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.15 — Very short patch repair (VSR) endonuclease

CATH v4.4 (1 domains)

Domain ID domain_id	1cw0A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	960 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — VSR Endonuclease

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Unit-cell length a length_a	63.000 Å
Unit-cell length b length_b	63.000 Å
Unit-cell length c length_c	152.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	22.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2300

CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA

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

PROTEIN (DNA MISMATCH ENDONUCLEASE)

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

1cw0__assembly_1__model_1

1cw0__assembly_1__model_1 | I(q)

1cw0__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA

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

PROTEIN (DNA MISMATCH ENDONUCLEASE)

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

1cw0__assembly_1__model_1

1cw0__assembly_1__model_1 | I(q)

1cw0__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)