1lnx

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)

Method: X-RAY DIFFRACTION

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

small nuclear ribonucleoprotein homolog (Sm-like)

Pyrobaculum aerophilum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 7	URIDINE × 7 GLYCEROL × 10 ACETIC ACID × 2 water × 7	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 14	URIDINE × 14 GLYCEROL × 20 ACETIC ACID × 4 water × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZYG5_PYRAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–80； UniProt 1–80 Author chain B； PDBConstruct 1–80； UniProt 1–80 Author chain C； PDBConstruct 1–80； UniProt 1–80 Author chain D； PDBConstruct 1–80； UniProt 1–80 Author chain E； PDBConstruct 1–80； UniProt 1–80 Author chain F； PDBConstruct 1–80； UniProt 1–80 Author chain G； PDBConstruct 1–80； UniProt 1–80

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	1lnx
Deposition date deposition_date	2002-05-04
Structure title title	Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)
Keywords keywords	beta barrel-like structure (OB fold); homoheptameric, RNA BINDING PROTEIN, transcription; RNA BINDING PROTEIN, transcription
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.

1lnx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1lnx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lnx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.57 Å
Rg (electron density)	28.53 Å
Total Rg	29.53 Å
Atom count	8388
Residues	1026
Excluded volume	149930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lnx__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1lnx__assembly_2__model_1`	tetradecameric （14）	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	small nuclear ribonucleoprotein homolog (Sm-like)
Molecular weight formula_weight	8937.3 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	4519

MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVPG

Source Source

Source organism organism	Pyrobaculum aerophilum
NCBI taxonomy ID ncbi_taxonomy_id	13773
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	URIDINE
Molecular weight formula_weight	244.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	325

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1lnxa1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1lnxa2
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	d1lnxb_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1lnxc_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1lnxd_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1lnxe_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1lnxf1
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1lnxf2
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	d1lnxg_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

CATH v4.4 (7 domains)

Domain ID domain_id	1lnxA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1lnxB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1lnxC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1lnxD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1lnxE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1lnxF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1lnxG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	91.829 Å
Unit-cell length b length_b	113.764 Å
Unit-cell length c length_c	126.594 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	56

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	19.780 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2260

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)

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

small nuclear ribonucleoprotein homolog (Sm-like)

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

1lnx__assembly_2__model_1

1lnx__assembly_2__model_1 | I(q)

1lnx__assembly_2__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (9 domains)

CATH v4.4 (7 domains)

7. Citations (2)

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)

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

small nuclear ribonucleoprotein homolog (Sm-like)

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

1lnx__assembly_2__model_1

1lnx__assembly_2__model_1 | I(q)

1lnx__assembly_2__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (9 domains)

CATH v4.4 (7 domains)

7. Citations (2)