SAXSdb — 2odi

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

R.BcnI

Brevibacillus centrosporus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(APAPCPCPCPGPGPAPGPAPC)-3' × 1 5'-D(CPTPCPCPGPGPGPTPTPGPT)-3' × 1 CALCIUM ION × 2 CHLORIDE ION × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(APAPCPCPCPGPGPAPGPAPC)-3' × 1 5'-D(CPTPCPCPGPGPGPTPTPGPT)-3' × 1 CALCIUM ION × 1 CHLORIDE ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RNV8_9BACL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–238； UniProt 1–238 Author chain B； PDBConstruct 1–238； UniProt 1–238

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	2odi
Deposition date deposition_date	2006-12-22
Structure title title	Restriction Endonuclease BCNI-Cognate DNA Substrate Complex
Keywords keywords	ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, BCNI, 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.

2odi__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2odi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2odi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.11 Å
Rg (electron density)	18.46 Å
Total Rg	19.24 Å
Atom count	2369
Residues	254
Excluded volume	41148 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2odi__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2odi__assembly_2__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	5'-D(APAPCPCPCPGPGPAPGPAP*C)-3'
Molecular weight formula_weight	3352.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E
Atom count atom_count	5583

AACCCGGAGAC

Entity 2 Entity 2 polymer

Description description	5'-D(CPTPCPCPGPGPGPTPTPGP*T)-3'
Molecular weight formula_weight	3356.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

CTCCGGGTTGT

Entity 3 Entity 3 polymer

Description description	R.BcnI
Molecular weight formula_weight	27616.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MKIWSKEEVVNKLHEIKNKGYLSVPTDMFRTDDGVVGQILERQFGVQENNITLGDLGEFELKGMRNRKAKSNLTLFHKKPVAGQTVIQIFNRFGYVKPSSRNPEVMKKKLFTTIKGGRLNNLGLTLNAKHASEINLYYQDEYLSTWDLNLSKIEKLVLVFAETIGRANSPEEQFHFTKAYMLTEINDITSLINDGVLVMDLCIDQDLSKSKGPHDRGPHLRIPISKLDKLYRNIERLL

Source Source

Source organism organism	Brevibacillus centrosporus
NCBI taxonomy ID ncbi_taxonomy_id	54910
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	650

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2odiA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily	20 — MvaI/BcnI restriction endonuclease, catalytic domain

Domain ID domain_id	2odiA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3570 — MvaI/BcnI restriction endonuclease, recognition domain

Domain ID domain_id	2odiB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily	20 — MvaI/BcnI restriction endonuclease, catalytic domain

Domain ID domain_id	2odiB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3570 — MvaI/BcnI restriction endonuclease, recognition domain

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Unit-cell length a length_a	81.553 Å
Unit-cell length b length_b	87.870 Å
Unit-cell length c length_c	79.391 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	28.380 Å
R factor r_factor	0.1750
R_work r_work	0.1740
R_free r_free	0.1990

Restriction Endonuclease BCNI-Cognate DNA Substrate Complex

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

R.BcnI

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

2odi__assembly_2__model_1

2odi__assembly_2__model_1 | I(q)

2odi__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Restriction Endonuclease BCNI-Cognate DNA Substrate Complex

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

R.BcnI

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

2odi__assembly_2__model_1

2odi__assembly_2__model_1 | I(q)

2odi__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)