SAXSdb — 2b3j

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

tRNA adenosine deaminase

Staphylococcus aureus subsp. aureus Mu50

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 2	anticodon stem-loop of t-RNA-Arg2 (nucleotides 27-42) × 2 ZINC ION × 2 GLYCEROL × 2 water × 4	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 2 RNA 2	anticodon stem-loop of t-RNA-Arg2 (nucleotides 27-42) × 2 ZINC ION × 2 GLYCEROL × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q99W51_STAAM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–159； UniProt 1–156 Author chain B； PDBConstruct 4–159； UniProt 1–156 Author chain C； PDBConstruct 4–159； UniProt 1–156 Author chain D； PDBConstruct 4–159； UniProt 1–156

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	2b3j
Deposition date deposition_date	2005-09-20
Structure title title	Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA
Keywords keywords	mixed alpha-beta, protein-rna complex, RNA stem-loop, HYDROLASE-RNA COMPLEX; HYDROLASE/RNA
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.

2b3j__assembly_2__model_1

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

Download this curve (.dat)

2b3j__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b3j__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.65 Å
Rg (electron density)	20.43 Å
Total Rg	21.13 Å
Atom count	2778
Residues	324
Excluded volume	47860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b3j__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2b3j__assembly_2__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	anticodon stem-loop of t-RNA-Arg2 (nucleotides 27-42)
Molecular weight formula_weight	5068.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,F,G,H
Atom count atom_count	5991

UUUGACUACGGAUCAA

Entity 2 Entity 2 polymer

Description description	tRNA adenosine deaminase
Molecular weight formula_weight	17394.1 kDa
EC 编号 ec_number	3.5.4.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GSHMTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRANKKSTN

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus Mu50
NCBI taxonomy ID ncbi_taxonomy_id	158878
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	300

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2b3ja1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.2 — Deoxycytidylate deaminase-like

Domain ID domain_id	d2b3jb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.2 — Deoxycytidylate deaminase-like

Domain ID domain_id	d2b3jc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.2 — Deoxycytidylate deaminase-like

Domain ID domain_id	d2b3jd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.2 — Deoxycytidylate deaminase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2b3jA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	2b3jB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	2b3jC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	2b3jD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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Unit-cell length a length_a	81.055 Å
Unit-cell length b length_b	89.029 Å
Unit-cell length c length_c	119.133 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	16

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	48.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2420

Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA

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

tRNA adenosine deaminase

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

2b3j__assembly_2__model_1

2b3j__assembly_2__model_1 | I(q)

2b3j__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA

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

tRNA adenosine deaminase

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

2b3j__assembly_2__model_1

2b3j__assembly_2__model_1 | I(q)

2b3j__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)