SAXSdb — 3c0w

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

Intron-encoded endonuclease I-SceI

Saccharomyces cerevisiae

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(DAPDCPDGPDCPDTPDAPDGPDGPDGPDAPDTPDAPDAPDCPDAPDGPDGPDGPDTPDAPDAPDTPDAPDC)-3') ; × 1 ;DNA (5'-D(DGPDTPDAPDTPDTPDAPDCPDCPDCPDTPDGPDTPDTPDAPDT)-3') ; × 1 ;DNA (5'-D(PDCPDCPDCPDTPDAPDGPDCPDGPDT)-3') ; × 1 CALCIUM ION × 3 SODIUM ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCE1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 1–235

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	3c0w
Deposition date deposition_date	2008-01-21
Structure title title	I-SceI in complex with a bottom nicked DNA substrate
Keywords keywords	;endonuclease, homing, LADLIDADG, catalytic mechanism, metal binding, nicked intermediate, Hydrolase, Intron homing, Mitochondrion, mRNA processing, mRNA splicing, 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.

3c0w__assembly_1__model_1

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

Download this curve (.dat)

3c0w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c0w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.08 Å
Rg (electron density)	21.83 Å
Total Rg	22.64 Å
Atom count	2837
Residues	271
Excluded volume	48024 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c0w__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(DAPDCPDGPDCPDTPDAPDGPDGPDGPDAPDTPDAPDAPDCPDAPDGPDGPDGPDTPDAPDAPDTPDAPDC)-3') ;
Molecular weight formula_weight	7451.8 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	2939

ACGCTAGGGATAACAGGGTAATAC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DGPDTPDAPDTPDTPDAPDCPDCPDCPDTPDGPDTPDTPDAP*DT)-3') ;
Molecular weight formula_weight	4550.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GTATTACCCTGTTAT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PDCPDCPDCPDTPDAPDGPDCPDGP*DT)-3') ;
Molecular weight formula_weight	2691.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CCCTAGCGT

Entity 4 Entity 4 polymer

Description description	Intron-encoded endonuclease I-SceI
Molecular weight formula_weight	27717.2 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

MKNIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLPNTISSETFLK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	98

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3c0wA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	3c0wA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

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Unit-cell length a length_a	80.610 Å
Unit-cell length b length_b	80.610 Å
Unit-cell length c length_c	127.090 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	28.000 Å
R factor r_factor	—
R_work r_work	0.2680
R_free r_free	0.2870

I-SceI in complex with a bottom nicked DNA substrate

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

Intron-encoded endonuclease I-SceI

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

3c0w__assembly_1__model_1

3c0w__assembly_1__model_1 | I(q)

3c0w__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

CATH v4.4 (2 domains)

7. Citations (1)

I-SceI in complex with a bottom nicked DNA substrate

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

Intron-encoded endonuclease I-SceI

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

3c0w__assembly_1__model_1

3c0w__assembly_1__model_1 | I(q)

3c0w__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

CATH v4.4 (2 domains)

7. Citations (1)