SAXSdb — 2czv

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

Ribonuclease P protein component 3

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ribonuclease P protein component 2 × 2 （O59150） octyl beta-D-glucopyranoside × 2 ACETIC ACID × 16 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP3_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 1–212 Author chain B； PDBConstruct 1–212； UniProt 1–212

Ribonuclease P protein component 2

Pyrococcus horikoshii

UniProt O59150

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ribonuclease P protein component 3 × 2 （O59543） octyl beta-D-glucopyranoside × 2 ACETIC ACID × 16 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP2_PYRHO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–120； UniProt 1–120 Author chain D； PDBConstruct 1–120； UniProt 1–120

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	2czv
Deposition date deposition_date	2005-07-19
Structure title title	Crystal structure of archeal RNase P protein ph1481p in complex with ph1877p
Keywords keywords	Ribonuclease, RNA binding protein, RNA recognition motif, Protein-protein complex, Hydrolase; HYDROLASE
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.

2czv__assembly_1__model_1

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

Download this curve (.dat)

2czv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2czv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.58 Å
Rg (electron density)	28.84 Å
Total Rg	29.58 Å
Atom count	5449
Residues	651
Excluded volume	99267 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2czv__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	Ribonuclease P protein component 3
Molecular weight formula_weight	24734.1 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5769

MVGGGGVKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILKRLKY

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribonuclease P protein component 2
Molecular weight formula_weight	14052.6 kDa
EC 编号 ec_number	3.1.26.5
Mutation mutation	C72S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MMRKLKTLPPTLRDKNRYIAFEIISDGDFTKDEVKELIWKSSLEVLGETGTAIVKPWLIKFDPNTKTGIVRSDREYVEYLRFALMLVSEFNGKRLIIRTLGVSGTIKRLKRKFLAKYGWK

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	320

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2czva_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.3 — PHP domain-like
Family Family family	c.6.3.2 — RNase P subunit p30

Domain ID domain_id	d2czvb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.6 — 7-stranded beta/alpha barrel
Superfamily Superfamily superfamily	c.6.3 — PHP domain-like
Family Family family	c.6.3.2 — RNase P subunit p30

Domain ID domain_id	d2czvc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.59 — Rnp2-like
Family Family family	d.58.59.1 — Rpp14/Pop5-like

Domain ID domain_id	d2czvd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.59 — Rnp2-like
Family Family family	d.58.59.1 — Rpp14/Pop5-like

CATH v4.4 (4 domains)

Domain ID domain_id	2czvA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2czvB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2czvC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3250 — Ribonuclease P, Pop5 subunit

Domain ID domain_id	2czvD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3250 — Ribonuclease P, Pop5 subunit

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Unit-cell length a length_a	63.332 Å
Unit-cell length b length_b	76.118 Å
Unit-cell length c length_c	151.276 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	48.690 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2610

Crystal structure of archeal RNase P protein ph1481p in complex with ph1877p

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

Ribonuclease P protein component 3

State in the Current Structure

Other States of the Same Protein in the Database

Ribonuclease P protein component 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

2czv__assembly_1__model_1

2czv__assembly_1__model_1 | I(q)

2czv__assembly_1__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

Source Source

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 archeal RNase P protein ph1481p in complex with ph1877p

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

Ribonuclease P protein component 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonuclease P protein component 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

2czv__assembly_1__model_1

2czv__assembly_1__model_1 | I(q)

2czv__assembly_1__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

Source Source

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)