SAXSdb — 1xaf

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

orf, conserved hypothetical protein

Shigella flexneri 2a

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 8 ACETATE ION × 5 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q83K13_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–246； UniProt 1–243 Author chain B； PDBConstruct 4–246； UniProt 1–243

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	1xaf
Deposition date deposition_date	2004-08-25
Structure title title	Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T
Keywords keywords	;Structural Genomics, Protein Structure Initiative, MCSG, Hypothetical protein, YfiH, Shigella flexneri 2a str. 2457T, PSI, Midwest Center for Structural Genomics, 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.

1xaf__assembly_1__model_1

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

Download this curve (.dat)

1xaf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xaf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.78 Å
Rg (electron density)	24.25 Å
Total Rg	24.94 Å
Atom count	3728
Residues	477
Excluded volume	66326 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xaf__assembly_1__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	orf, conserved hypothetical protein
Molecular weight formula_weight	26823.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4148

SNAMSKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI

Source Source

Source organism organism	Shigella flexneri 2a
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	8

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	420

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xafa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.194 — CNF1/YfiH-like putative cysteine hydrolases
Superfamily Superfamily superfamily	d.194.1 — CNF1/YfiH-like putative cysteine hydrolases
Family Family family	d.194.1.2 — YfiH-like

Domain ID domain_id	d1xafb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.194 — CNF1/YfiH-like putative cysteine hydrolases
Superfamily Superfamily superfamily	d.194.1 — CNF1/YfiH-like putative cysteine hydrolases
Family Family family	d.194.1.2 — YfiH-like

CATH v4.4 (2 domains)

Domain ID domain_id	1xafA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	140 — CNF1/YfiH-like putative cysteine hydrolases
Homologous superfamily homologous superfamily	10 — CNF1/YfiH-like putative cysteine hydrolases

Domain ID domain_id	1xafB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	140 — CNF1/YfiH-like putative cysteine hydrolases
Homologous superfamily homologous superfamily	10 — CNF1/YfiH-like putative cysteine hydrolases

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Unit-cell length a length_a	43.874 Å
Unit-cell length b length_b	50.583 Å
Unit-cell length c length_c	55.347 Å
Unit-cell angle α angle_alpha	90.32 °
Unit-cell angle β angle_beta	96.32 °
Unit-cell angle γ angle_gamma	90.40 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	55.050 Å
R factor r_factor	0.1858
R_work r_work	0.1786
R_free r_free	0.2516

Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T

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

orf, conserved hypothetical protein

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

1xaf__assembly_1__model_1

1xaf__assembly_1__model_1 | I(q)

1xaf__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T

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

orf, conserved hypothetical protein

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

1xaf__assembly_1__model_1

1xaf__assembly_1__model_1 | I(q)

1xaf__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)