SAXSdb — 3erj

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

Peptidyl-tRNA hydrolase

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTH_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 1–115 Author chain B； PDBConstruct 1–115； UniProt 1–115

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	3erj
Deposition date deposition_date	2008-10-02
Structure title title	Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4
Keywords keywords	;alpha-beta, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Cytoplasm, 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.

3erj__assembly_1__model_1

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

Download this curve (.dat)

3erj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3erj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.22 Å
Rg (electron density)	16.92 Å
Total Rg	18.06 Å
Atom count	1734
Residues	227
Excluded volume	31769 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3erj__assembly_1__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3erja2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.1 — Peptidyl-tRNA hydrolase II

Domain ID domain_id	d3erja3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3erjb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.1 — Peptidyl-tRNA hydrolase II

CATH v4.4 (2 domains)

Domain ID domain_id	3erjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	3erjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

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Unit-cell length a length_a	43.903 Å
Unit-cell length b length_b	46.925 Å
Unit-cell length c length_c	105.263 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	1.800 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2240

Description description	Peptidyl-tRNA hydrolase
Molecular weight formula_weight	13578.9 kDa
EC 编号 ec_number	3.1.1.29
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1886

Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4

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

Peptidyl-tRNA 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

3erj__assembly_1__model_1

3erj__assembly_1__model_1 | I(q)

3erj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	152

Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4

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

Peptidyl-tRNA 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

3erj__assembly_1__model_1

3erj__assembly_1__model_1 | I(q)

3erj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)