8ctz

12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H

Method: X-RAY DIFFRACTION

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

Ribonuclease H

Alkalihalobacillus halodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 3 DNA 2	;DNA (5'-D(CPGPCP(6OG)PAPAPTPTP(OWR)PGPCPG)-3') ; × 2 GLYCEROL × 4 1,2-ETHANEDIOL × 3 ACETATE ION × 2 SODIUM ION × 1 POTASSIUM ION × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNH1_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–142； UniProt 59–196 Author chain B； PDBConstruct 5–142； UniProt 59–196 Author chain C； PDBConstruct 5–142； UniProt 59–196

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	8ctz
Deposition date deposition_date	2022-05-16
Structure title title	12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H
Keywords keywords	;alkylation, base stacking, DNA damage, H-bonding, O6-methyl-2'-deoxyguanosine, ExBIM, DNA ;; 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.

8ctz__assembly_1__model_1

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

Download this curve (.dat)

8ctz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ctz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.38 Å
Rg (electron density)	27.31 Å
Total Rg	27.92 Å
Atom count	3726
Residues	412
Excluded volume	65199 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ctz__assembly_1__model_1`	pentameric （5）	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 (8)

Entity 1 Entity 1 polymer

Description description	Ribonuclease H
Molecular weight formula_weight	16329.5 kDa
EC 编号 ec_number	3.1.26.4
Mutation mutation	D132N
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	3845

GSHMAKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK

Source Source

Source organism organism	Alkalihalobacillus halodurans
NCBI taxonomy ID ncbi_taxonomy_id	86665
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPGPCP(6OG)PAPAPTPTP(OWR)PGPCPG)-3') ;
Molecular weight formula_weight	3734.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E

CGCGAATTXGCG

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

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 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

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Unit-cell length a length_a	59.506 Å
Unit-cell length b length_b	66.492 Å
Unit-cell length c length_c	69.182 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.320 Å
Low-resolution limit resolution_low	29.740 Å
R factor r_factor	0.1988
R_work r_work	0.1954
R_free r_free	0.2651

12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H

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

Ribonuclease H

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

8ctz__assembly_1__model_1

8ctz__assembly_1__model_1 | I(q)

8ctz__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H

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

Ribonuclease H

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

8ctz__assembly_1__model_1

8ctz__assembly_1__model_1 | I(q)

8ctz__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)