SAXSdb — 3c8g

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

Putative transcriptional regulator

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 2	ACETATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 1	Consistent with protein count
3	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	Q83Q96_SHIFL
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 4–172； UniProt 1–169 Author chain C； PDBConstruct 4–172； UniProt 1–169 Author chain B； PDBConstruct 4–172； UniProt 1–169 Author chain D； PDBConstruct 4–172； UniProt 1–169

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	3c8g
Deposition date deposition_date	2008-02-12
Structure title title	Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T
Keywords keywords	;APC27974, YggD, Mannitol operon repressor, Shigella flexneri 2a str. 2457T, methylation, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSCRIPTION REGULATOR ;; TRANSCRIPTION REGULATOR
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.

3c8g__assembly_2__model_1

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

Download this curve (.dat)

3c8g__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c8g__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.36 Å
Rg (electron density)	27.05 Å
Total Rg	27.59 Å
Atom count	2696
Residues	312
Excluded volume	48555 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c8g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c8g__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3c8g__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Putative transcriptional regulator
Molecular weight formula_weight	19893.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5350

SNAMATLTEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELTP

Source Source

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

Entity 2 Entity 2 polymer

Description description	Putative transcriptional regulator
Molecular weight formula_weight	19893.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNAMATLTEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELTP

Source Source

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

Entity 3 Entity 3 polymer

Description description	Putative transcriptional regulator
Molecular weight formula_weight	19839.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SNAMATLTEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELTP

Source Source

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

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3c8ga1
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

Domain ID domain_id	d3c8ga2
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	d3c8gb1
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

Domain ID domain_id	d3c8gc2
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

Domain ID domain_id	d3c8gc3
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	d3c8gd1
Class class	a — All alpha proteins
Fold Fold fold	a.285 — MtlR-like
Superfamily Superfamily superfamily	a.285.1 — MtlR-like
Family Family family	a.285.1.1 — MtlR-like

CATH v4.4 (4 domains)

Domain ID domain_id	3c8gA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3c8gB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3c8gC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3c8gD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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Unit-cell length a length_a	71.365 Å
Unit-cell length b length_b	70.946 Å
Unit-cell length c length_c	159.037 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	31.810 Å
R factor r_factor	0.2116
R_work r_work	0.2067
R_free r_free	0.2703

Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T

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

Putative transcriptional regulator

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

3c8g__assembly_2__model_1

3c8g__assembly_2__model_1 | I(q)

3c8g__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T

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

Putative transcriptional regulator

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

3c8g__assembly_2__model_1

3c8g__assembly_2__model_1 | I(q)

3c8g__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)