SAXSdb — 3u6y

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

DNA/RNA-binding protein Alba 2

Aeropyrum pernix

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(CPCPGPGPC)-3') ; × 1 ;DNA (5'-D(GPGPCPCPG)-3') ; × 1 PHOSPHATE ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALBA2_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–102； UniProt 1–102 Author chain C； PDBConstruct 1–102； UniProt 1–102

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	3u6y
Deposition date deposition_date	2011-10-13
Structure title title	Crystal structure of ALBA2-DNA complex
Keywords keywords	;ALBA 2, Archaea, DNA-Binding Protein, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

3u6y__assembly_1__model_1

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

Download this curve (.dat)

3u6y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u6y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.22 Å
Rg (electron density)	19.65 Å
Total Rg	20.52 Å
Atom count	1750
Residues	208
Excluded volume	30628 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u6y__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 (5)

Entity 1 Entity 1 polymer

Description description	DNA/RNA-binding protein Alba 2
Molecular weight formula_weight	11397.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1933

MACEGAPEVRIGRKPVMNYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFAKNIEIKDIKIDSQEIEVQTPEGQTRTRRVSSIEICLEKAGESA

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPCPGPGP*C)-3') ;
Molecular weight formula_weight	1481.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CCGGC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPGPCPCP*G)-3') ;
Molecular weight formula_weight	1521.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

GGCCG

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	183

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3u6ya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.6 — AlbA-like
Family Family family	d.68.6.0 — automated matches

Domain ID domain_id	d3u6yc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.6 — AlbA-like
Family Family family	d.68.6.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3u6yA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

Domain ID domain_id	3u6yC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

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Unit-cell length a length_a	33.556 Å
Unit-cell length b length_b	74.290 Å
Unit-cell length c length_c	88.198 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.2820

Crystal structure of ALBA2-DNA complex

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

DNA/RNA-binding protein Alba 2

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

3u6y__assembly_1__model_1

3u6y__assembly_1__model_1 | I(q)

3u6y__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Crystal structure of ALBA2-DNA complex

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

DNA/RNA-binding protein Alba 2

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

3u6y__assembly_1__model_1

3u6y__assembly_1__model_1 | I(q)

3u6y__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)