SAXSdb — 8sv3

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

Ribonuclease H

Halalkalibacterium halodurans

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	Modified DNA × 2 MAGNESIUM ION × 1 GLYCEROL × 1 water × 3	Consistent with all polymers
2	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count

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	8sv3
Deposition date deposition_date	2023-05-15
Structure title title	7-Deazapurines and 5-Halogenpyrimidine DNA duplex
Keywords keywords	;7-Deazapurines, 5-Halogenpyrimidines, Adenine-Tract Geometry, RNase-H complex, DNA duplex, Dickerson-Drew Dodecamer, DNA duplex crystal structure, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/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.

8sv3__assembly_1__model_1

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

Download this curve (.dat)

8sv3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8sv3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.22 Å
Rg (electron density)	18.16 Å
Total Rg	19.11 Å
Atom count	1577
Residues	132
Excluded volume	26694 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8sv3__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8sv3__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8sv3__assembly_3__model_1`	monomeric （1）	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	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	4329

GSHMAKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK

Source Source

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

Entity 2 Entity 2 polymer

Description description	Modified DNA
Molecular weight formula_weight	3690.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E

XGCGAAUUCGCG

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	492

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Unit-cell length a length_a	36.983 Å
Unit-cell length b length_b	89.000 Å
Unit-cell length c length_c	72.566 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.44 °
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	1.510 Å
Low-resolution limit resolution_low	44.540 Å
R factor r_factor	0.1786
R_work r_work	0.1770
R_free r_free	0.2097

7-Deazapurines and 5-Halogenpyrimidine DNA duplex

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

8sv3__assembly_1__model_1

8sv3__assembly_1__model_1 | I(q)

8sv3__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 (6)

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 water

7. Citations (1)

7-Deazapurines and 5-Halogenpyrimidine DNA duplex

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

8sv3__assembly_1__model_1

8sv3__assembly_1__model_1 | I(q)

8sv3__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 (6)

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 water

7. Citations (1)