1y2i

Crystal Structure of MCSG Target APC27401 from Shigella flexneri

Method: X-RAY DIFFRACTION

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

Hypothetical Protein S0862

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 5	water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q83LS2_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–131； UniProt 1–107 Author chain B； PDBConstruct 25–131； UniProt 1–107 Author chain C； PDBConstruct 25–131； UniProt 1–107 Author chain D； PDBConstruct 25–131； UniProt 1–107 Author chain E； PDBConstruct 25–131； UniProt 1–107

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	1y2i
Deposition date deposition_date	2004-11-22
Structure title title	Crystal Structure of MCSG Target APC27401 from Shigella flexneri
Keywords keywords	;Structural Genomics, Pentamer, Hypothetical Protein, Protein Structure Initiative, PSI, Midwest Center for Structural Genomics, MCSG, unknown function ;; Structural Genomics, unknown function
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.

1y2i__assembly_1__model_1

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

Download this curve (.dat)

1y2i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y2i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.30 Å
Rg (electron density)	22.08 Å
Total Rg	23.01 Å
Atom count	4085
Residues	530
Excluded volume	72836 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y2i__assembly_1__model_1`	pentameric （5）	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) 15 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1y2ia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.5 — YbjQ-like
Family Family family	d.230.5.1 — YbjQ-like

Domain ID domain_id	d1y2ia2
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	d1y2ib1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.5 — YbjQ-like
Family Family family	d.230.5.1 — YbjQ-like

Domain ID domain_id	d1y2ib2
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	d1y2ic1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.5 — YbjQ-like
Family Family family	d.230.5.1 — YbjQ-like

Domain ID domain_id	d1y2ic2
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	d1y2id1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.5 — YbjQ-like
Family Family family	d.230.5.1 — YbjQ-like

Domain ID domain_id	d1y2id2
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	d1y2ie1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.5 — YbjQ-like
Family Family family	d.230.5.1 — YbjQ-like

Domain ID domain_id	d1y2ie2
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 (5 domains)

Domain ID domain_id	1y2iA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	70 — Hypothetical protein apc22750. Chain B

Domain ID domain_id	1y2iB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	70 — Hypothetical protein apc22750. Chain B

Domain ID domain_id	1y2iC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	70 — Hypothetical protein apc22750. Chain B

Domain ID domain_id	1y2iD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	70 — Hypothetical protein apc22750. Chain B

Domain ID domain_id	1y2iE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	70 — Hypothetical protein apc22750. Chain B

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Unit-cell length a length_a	56.918 Å
Unit-cell length b length_b	79.200 Å
Unit-cell length c length_c	109.620 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	20

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1955
R_work r_work	0.1922
R_free r_free	0.2555

Description description	Hypothetical Protein S0862
Molecular weight formula_weight	14544.8 kDa
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	4511

Crystal Structure of MCSG Target APC27401 from Shigella flexneri

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

Hypothetical Protein S0862

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

1y2i__assembly_1__model_1

1y2i__assembly_1__model_1 | I(q)

1y2i__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) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	361

Crystal Structure of MCSG Target APC27401 from Shigella flexneri

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

Hypothetical Protein S0862

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

1y2i__assembly_1__model_1

1y2i__assembly_1__model_1 | I(q)

1y2i__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) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)