SAXSdb — 3q1q

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

Ribonuclease P protein component

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 2	RNase P RNA × 1 TRNA (PHE) × 1 MAGNESIUM ION × 4 PHOSPHATE ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNPA_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–118； UniProt 3–117

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	3q1q
Deposition date deposition_date	2010-12-17
Structure title title	Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA
Keywords keywords	;RNase P, ribozyme, ribonuclease P, tRNA, pre-tRNA, tetraloop-receptor, ribose zipper, a-minor interaction, base stacking, intermolecular base pairs, intermolecular RNA-RNA contacts, RNP, ribonucleoprotein complex, enzyme-product complex, metalloenzyme, RNA-metal interactions, shape complementarity, hydrolase-RNA complex, endonuclease ;; 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.

3q1q__assembly_1__model_1

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

Download this curve (.dat)

3q1q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3q1q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.48 Å
Rg (electron density)	41.55 Å
Total Rg	41.70 Å
Atom count	10155
Residues	545
Excluded volume	147190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3q1q__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	RNase P RNA
Molecular weight formula_weight	112622.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	10155

GGAGAGGAGCAGGCGGUCGCGGGGGCGCACACCUGCGCUUCCCGAGGAAAGUCCGGACUCUGGAGCGGGGUGCCGGGUAACGCCCGGGAGGGGUGACCCUCGGACAGGGCCAUAGAGAAGAAGACCGCCCGGGGGGAAACUUCCGGGCAAGGGUGGAACGGUGGGGUAAGAGCCCACCAGCGUCGGGGCAACCCGGCGGCUUGGCAACCCCCACCUGGAGCAAGGCCAAGCAGGGGGUUGGGUCGCUCCCCCUAUUCCCCCGGGUUGGCCGCUUGAGGUGUGCGGUAACGCACACCCCAGAUUGAUGACCGCCCACGACAGAAUCCGGCUUAUGCUCCUCUCCCGUG

Entity 2 Entity 2 polymer

Description description	Ribonuclease P protein component
Molecular weight formula_weight	14363.0 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GSTESFTRRERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	TRNA (PHE)
Molecular weight formula_weight	27658.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

GGCCAGGUAGCUCAGUUGGUAGAGCACUGGAUAUGGGCACCCCCUAAGUCCAGGUGUCGGCGGUUCGAUUCCGCCCCUGGCCACCA

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3q1qA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	169.290 Å
Unit-cell length b length_b	169.290 Å
Unit-cell length c length_c	184.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	28.970 Å
R factor r_factor	0.2510
R_work r_work	0.2500
R_free r_free	0.2720

Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA

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

Ribonuclease P protein component

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

3q1q__assembly_1__model_1

3q1q__assembly_1__model_1 | I(q)

3q1q__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA

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

Ribonuclease P protein component

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

3q1q__assembly_1__model_1

3q1q__assembly_1__model_1 | I(q)

3q1q__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)