1ylo

Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 from Shigella flexneri 2a str. 2457T

Method: X-RAY DIFFRACTION

▼

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

hypothetical protein SF2450

Shigella flexneri 2a str. 2457T

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	Q83K87_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–348； UniProt 1–345 Author chain B； PDBConstruct 4–348； UniProt 1–345 Author chain C； PDBConstruct 4–348； UniProt 1–345 Author chain D； PDBConstruct 4–348； UniProt 1–345 Author chain E； PDBConstruct 4–348； UniProt 1–345 Author chain F； PDBConstruct 4–348； UniProt 1–345

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ylo
Deposition date deposition_date	2005-01-19
Structure title title	Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 from Shigella flexneri 2a str. 2457T
Keywords keywords	;structural genomics, MCSG, hypothetical protein S2589, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1ylo__assembly_1__model_1

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

Download this curve (.dat)

1ylo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ylo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.53 Å
Rg (electron density)	48.23 Å
Total Rg	48.24 Å
Atom count	31500
Residues	4008
Excluded volume	562270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ylo__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	hypothetical protein SF2450
Molecular weight formula_weight	38313.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16577

SNAMDLSLLKALSEADAIASSEQEVRQILLEEAARLQKEVRFDGLGSVLIRLNESTGPKVMICAHMDEVGFMVRSISREGAIDVLPVGNVRMAARQLQPVRITTREECKIPGLLDGDRQGNDVSAMRVDIGARTYDEVMQAGIRPGDRVTFDTTFQVLPHQRVMGKAFDDRLSCYLLVTLLRELHDAELPAEVWLVASSSEEVGLRGGQTATRAVSPDVAIVLDTACWAKNFDYGAANHRQIGNGPMLVLSDKSLIAPPKLTAWIETVAAEIGVPLQADMFSNGGTDGGAVHLTGTGVPTLVMGPATRHGHCAASIADCRDILQMEQLLSALIQRLTRETVVQLTDFR

Source Source

Source organism organism	Shigella flexneri 2a str. 2457T
NCBI taxonomy ID ncbi_taxonomy_id	198215
Host organism host_organism	Escherichia coli BL21(DE3)

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	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	677

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d1yloa1
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	d1yloa2
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	d1yloa3
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	d1ylob1
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	d1ylob2
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	d1ylob3
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	d1yloc1
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	d1yloc2
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	d1yloc3
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	d1ylod1
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	d1ylod2
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	d1ylod3
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	d1yloe1
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	d1yloe2
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	d1yloe3
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	d1ylof1
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	d1ylof2
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	d1ylof3
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

CATH v4.4 (12 domains)

Domain ID domain_id	1yloA01
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	1yloA02
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	1yloB01
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	1yloB02
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	1yloC01
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	1yloC02
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	1yloD01
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	1yloD02
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	1yloE01
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	1yloE02
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	1yloF01
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	1yloF02
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

▶

Unit-cell length a length_a	161.827 Å
Unit-cell length b length_b	161.827 Å
Unit-cell length c length_c	228.574 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	48

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1923
R_work r_work	0.1903
R_free r_free	0.2289

Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 from Shigella flexneri 2a str. 2457T

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

hypothetical protein SF2450

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

1ylo__assembly_1__model_1

1ylo__assembly_1__model_1 | I(q)

1ylo__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) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 from Shigella flexneri 2a str. 2457T

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

hypothetical protein SF2450

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

1ylo__assembly_1__model_1

1ylo__assembly_1__model_1 | I(q)

1ylo__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) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (1)