SAXSdb — 3t3n

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

Metal dependent hydrolase

Thermus thermophilus HB27

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	O2'methyl-RNA × 2 ZINC ION × 2 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72JJ7_THET2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–562； UniProt 20–572

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	3t3n
Deposition date deposition_date	2011-07-25
Structure title title	Molecular basis for the recognition and cleavage of RNA (UUCCGU) by the bifunctional 5'-3' exo/endoribonuclease RNase J
Keywords keywords	;PROTEIN-RNA COMPLEX, Metallo-beta-lactamase, RNase J, Endoribonuclease, 5'-3' Exoribonuclease, Metal dependent hydrolase, RNA, hydrolase, 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.

3t3n__assembly_1__model_1

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

Download this curve (.dat)

3t3n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3t3n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.84 Å
Rg (electron density)	32.24 Å
Total Rg	32.85 Å
Atom count	8884
Residues	1100
Excluded volume	158990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3t3n__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 (4)

Entity 1 Entity 1 polymer

Description description	Metal dependent hydrolase
Molecular weight formula_weight	62612.4 kDa
EC 编号 ec_number	3.-.-.-
Mutation mutation	H77A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4455

MSHHHHHHSSQGGPQDHVEIIPLGGMGEIGKNITVFRFRDEIFVLDGGLAFPEEGMPGVDLLIPRVDYLIEHRHKIKAWVLTHGAEDHIGGLPFLLPMIFGKESPVPIYGARLTLGLLRGKLEEFGLRPGAFNLKEISPDDRIQVGRYFTLDLFRMTHSIPDNSGVVIRTPIGTIVHTGDFKLDPTPIDGKVSHLAKVAQAGAEGVLLLIADATNAERPGYTPSEMEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEKYGRKVAMEGRSMLKFSRIALELGYLKVKDRLYTLEEVKDLPDHQVLILATGSQGQPMSVLHRLAFEGHAKMAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYVLYPPTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQMNFKWLAESMSRPPEKTLIGENGAVYRLTRETFEKVGEVPHGVLYVDGLGVGDITEEILADRRHMAEEGLVVITALAGEDPVVEVVSRGFVKAGERLLGEVRRMALEALKNGVREKKPLERIRDDIYYPVKKFLKKATGRDPMILPVVIE

Source Source

Source organism organism	Thermus thermophilus HB27
NCBI taxonomy ID ncbi_taxonomy_id	262724
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	O2'methyl-RNA
Molecular weight formula_weight	1913.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

UUCCGU

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3t3nA01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	3t3nA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10710 — Metallo-hydrolase/oxidoreductase

Domain ID domain_id	3t3nA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	580 —

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Unit-cell length a length_a	101.950 Å
Unit-cell length b length_b	116.780 Å
Unit-cell length c length_c	231.280 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	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	3.090 Å
Low-resolution limit resolution_low	54.410 Å
R factor r_factor	0.2066
R_work r_work	0.2019
R_free r_free	0.2597

Molecular basis for the recognition and cleavage of RNA (UUCCGU) by the bifunctional 5'-3' exo/endoribonuclease RNase J

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

Metal dependent hydrolase

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

3t3n__assembly_1__model_1

3t3n__assembly_1__model_1 | I(q)

3t3n__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Molecular basis for the recognition and cleavage of RNA (UUCCGU) by the bifunctional 5'-3' exo/endoribonuclease RNase J

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

Metal dependent hydrolase

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

3t3n__assembly_1__model_1

3t3n__assembly_1__model_1 | I(q)

3t3n__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)