3iem

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog

Method: X-RAY DIFFRACTION

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

Ribonuclease TTHA0252

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 4	;RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3') ; × 4 SULFATE ION × 17 ZINC ION × 2 water × 4	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 2	;RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3') ; × 2 SULFATE ION × 19 ZINC ION × 2 CITRATE ANION × 1 water × 2	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 2	;RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3') ; × 2 SULFATE ION × 12 ZINC ION × 2 water × 2	Consistent with all polymers
4	Protein–RNA	Monomer	Protein 1 RNA 2	;RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3') ; × 2 SULFATE ION × 11 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	RNSE_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–431； UniProt 1–431 Author chain B； PDBConstruct 1–431； UniProt 1–431 Author chain C； PDBConstruct 1–431； UniProt 1–431 Author chain D； PDBConstruct 1–431； UniProt 1–431

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	3iem
Deposition date deposition_date	2009-07-23
Structure title title	Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog
Keywords keywords	metallo beta lactamase fold, Endonuclease, Hydrolase, Metal-binding, Nuclease, RNA-binding, rRNA processing, 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.

3iem__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3iem__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3iem__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	22.84 Å
Rg (electron density)	21.70 Å
Total Rg	22.59 Å
Atom count	3446
Residues	431
Excluded volume	60973 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3iem__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3iem__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3iem__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3iem__assembly_4__model_1`	trimeric （3）	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 TTHA0252
Molecular weight formula_weight	47118.1 kDa
EC 编号 ec_number	3.1.-.-
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
Atom count atom_count	14354

MRIVPFGAAREVTGSAHLLLAGGRRVLLDCGMFQGKEEARNHAPFGFDPKEVDAVLLTHAHLDHVGRLPKLFREGYRGPVYATRATVLLMEIVLEDALKVMDEPFFGPEDVEEALGHLRPLEYGEWLRLGALSLAFGQAGHLPGSAFVVAQGEGRTLVYSGDLGNREKDVLPDPSLPPLADLVLAEGTYGDRPHRPYRETVREFLEILEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLPRAPIYLDSPMAGRVLSLYPRLVRYFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLKHGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEEVPLRASVHTLGGFSGHAGQDELLDWLQGEPRVVLVHGEEEKLLALGKLLALRGQEVSLARFGEGVPV

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3') ;
Molecular weight formula_weight	1888.4 kDa
Source method src_method	syn
Copy count entity_count	10

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,H,I,J,K,L,M,N,O,P

UUUUUU

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	59

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 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	224

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3iema_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.10 — beta-CASP RNA-metabolising hydrolases

Domain ID domain_id	d3iemb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.10 — beta-CASP RNA-metabolising hydrolases

Domain ID domain_id	d3iemc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.10 — beta-CASP RNA-metabolising hydrolases

Domain ID domain_id	d3iemd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.10 — beta-CASP RNA-metabolising hydrolases

CATH v4.4 (8 domains)

Domain ID domain_id	3iemA01
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	3iemA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

Domain ID domain_id	3iemB01
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	3iemB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

Domain ID domain_id	3iemC01
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	3iemC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

Domain ID domain_id	3iemD01
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	3iemD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

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Unit-cell length a length_a	144.694 Å
Unit-cell length b length_b	146.441 Å
Unit-cell length c length_c	119.975 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2130
R_free r_free	0.2570

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog

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

Ribonuclease TTHA0252

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

3iem__assembly_3__model_1

3iem__assembly_3__model_1 | I(q)

3iem__assembly_3__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog

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

Ribonuclease TTHA0252

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

3iem__assembly_3__model_1

3iem__assembly_3__model_1 | I(q)

3iem__assembly_3__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)