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3imb

Alternative binding mode of restriction endonuclease BcnI to cognate DNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

R.BcnI

Brevibacillus centrosporus

UniProt Q8RNV8

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(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' × 1 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' × 1 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' × 1 water × 3 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' × 1 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' × 1 water × 3 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' × 1 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2odh

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2odi 2odi 2q10 2q10 3imb 3imb 3imb 3imb

8 assemblies

View Construct and Data Evidence
UniProt name Q8RNV8_9BACL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–238； UniProt 1–238 Author chain B； PDBConstruct 1–238； UniProt 1–238 Author chain C； PDBConstruct 1–238； UniProt 1–238 Author chain D； 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_id3imb
Deposition date deposition_date2009-08-10
Structure title titleAlternative binding mode of restriction endonuclease BcnI to cognate DNA
Keywords keywordsENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, BCNI, PSEUDOPALINDROMIC SEQUENCE RECOGNITION, PSEUDOSYMMETRY, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
Experimental Method methodX-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.

3imb__assembly_2__model_1

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

Download this curve (.dat)

3imb__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3imb__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）18.80 Å
Rg (electron density)18.22 Å
Total Rg19.05 Å
Atom count2285
Residues256
Excluded volume39762 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3imb__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3imb__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3imb__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3imb__assembly_4__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 (4)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3imbA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily20 — MvaI/BcnI restriction endonuclease, catalytic domain
Domain ID domain_id3imbA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3570 — MvaI/BcnI restriction endonuclease, recognition domain
Domain ID domain_id3imbB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily20 — MvaI/BcnI restriction endonuclease, catalytic domain
Domain ID domain_id3imbB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3570 — MvaI/BcnI restriction endonuclease, recognition domain
Domain ID domain_id3imbC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily20 — MvaI/BcnI restriction endonuclease, catalytic domain
Domain ID domain_id3imbC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3570 — MvaI/BcnI restriction endonuclease, recognition domain
Domain ID domain_id3imbD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily20 — MvaI/BcnI restriction endonuclease, catalytic domain
Domain ID domain_id3imbD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3570 — MvaI/BcnI restriction endonuclease, recognition domain
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7. Citations (3)