1xfo

Crystal Structure of an archaeal aminopeptidase

Method: X-RAY DIFFRACTION

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

Frv operon protein FrvX

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	ZINC ION × 24 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59196_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–357； UniProt 1–353 Author chain B； PDBConstruct 5–357； UniProt 1–353 Author chain C； PDBConstruct 5–357； UniProt 1–353 Author chain D； PDBConstruct 5–357； UniProt 1–353

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	1xfo
Deposition date deposition_date	2004-09-15
Structure title title	Crystal Structure of an archaeal aminopeptidase
Keywords keywords	aminopeptidase, self-compartmentalizing, metalloprotease, dinuclear, 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.

1xfo__assembly_1__model_1

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

Download this curve (.dat)

1xfo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xfo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.26 Å
Rg (electron density)	48.41 Å
Total Rg	48.74 Å
Atom count	31566
Residues	4071
Excluded volume	568190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xfo__assembly_1__model_1`	dodecameric （12）	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 (3)

Entity 1 Entity 1 polymer

Description description	Frv operon protein FrvX
Molecular weight formula_weight	39510.5 kDa
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	11167

RGSHMEVRNMVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVPPHIQKPEDRKKAPDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI

Source Source

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

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	645

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1xfoa1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
Family Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

Domain ID domain_id	d1xfoa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1xfoa3
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	d1xfob1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
Family Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

Domain ID domain_id	d1xfob2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1xfoc1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
Family Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

Domain ID domain_id	d1xfoc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1xfod1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.3 — Aminopeptidase/glucanase lid domain
Family Family family	b.49.3.1 — Aminopeptidase/glucanase lid domain

Domain ID domain_id	d1xfod2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

CATH v4.4 (8 domains)

Domain ID domain_id	1xfoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1xfoA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

Domain ID domain_id	1xfoB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1xfoB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

Domain ID domain_id	1xfoC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1xfoC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

Domain ID domain_id	1xfoD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1xfoD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	40 — Peptidase M42, domain 2

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Unit-cell length a length_a	158.340 Å
Unit-cell length b length_b	158.340 Å
Unit-cell length c length_c	114.460 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	24

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	29.920 Å
R factor r_factor	0.1834
R_work r_work	0.1828
R_free r_free	0.2093

Crystal Structure of an archaeal aminopeptidase

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

Frv operon protein FrvX

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

1xfo__assembly_1__model_1

1xfo__assembly_1__model_1 | I(q)

1xfo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of an archaeal aminopeptidase

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

Frv operon protein FrvX

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

1xfo__assembly_1__model_1

1xfo__assembly_1__model_1 | I(q)

1xfo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)