SAXSdb — 4ryu

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

;5'/3'-nucleotidase SurE ;

Salmonella enterica subsp. enterica serovar Enteritidis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 6 MAGNESIUM ION × 2 GLYCEROL × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 2 MAGNESIUM ION × 2 GLYCEROL × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SURE_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–267； UniProt 1–253 Author chain B； PDBConstruct 15–267； UniProt 1–253 Author chain C； PDBConstruct 15–267； UniProt 1–253 Author chain D； PDBConstruct 15–267； UniProt 1–253

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	4ryu
Deposition date deposition_date	2014-12-17
Structure title title	Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium
Keywords keywords	Stationary phase survival protein, Domain swapping, Rossmann fold like, Phosphatase, HYDROLASE; HYDROLASE
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.

4ryu__assembly_1__model_1

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

Download this curve (.dat)

4ryu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ryu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.87 Å
Rg (electron density)	23.01 Å
Total Rg	23.78 Å
Atom count	3873
Residues	513
Excluded volume	68082 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ryu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ryu__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	;5'/3'-nucleotidase SurE ;
Molecular weight formula_weight	28557.1 kDa
EC 编号 ec_number	3.1.3.5, 3.1.3.6
Mutation mutation	E112A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8749

MRGSHHHHHHGMASMRILLSNDDGVHAPGIQTLAKALREFADVQVVAPDRNRSGASNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYLGVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMAGRHLGFPALAVSLNGYQHYDTAAAVTCALLRGLSREPLRTGRILNVNVPDLPLAQVKGIRVTRCGSRHPADKVIPQEDPRGNTLYWIGPPGDKYDAGPDTDFAAVDEGYVSVTPLHVDLTAHSAHDVVSDWLDSVGVGTQW

Source Source

Source organism organism	Salmonella enterica subsp. enterica serovar Enteritidis
NCBI taxonomy ID ncbi_taxonomy_id	1412588
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	933

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4ryua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.106 — SurE-like
Superfamily Superfamily superfamily	c.106.1 — SurE-like
Family Family family	c.106.1.0 — automated matches

Domain ID domain_id	d4ryua2
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	d4ryub1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.106 — SurE-like
Superfamily Superfamily superfamily	c.106.1 — SurE-like
Family Family family	c.106.1.0 — automated matches

Domain ID domain_id	d4ryub2
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	d4ryuc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.106 — SurE-like
Superfamily Superfamily superfamily	c.106.1 — SurE-like
Family Family family	c.106.1.0 — automated matches

Domain ID domain_id	d4ryuc2
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	d4ryud1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.106 — SurE-like
Superfamily Superfamily superfamily	c.106.1 — SurE-like
Family Family family	c.106.1.0 — automated matches

Domain ID domain_id	d4ryud2
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 (4 domains)

Domain ID domain_id	4ryuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
Homologous superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

Domain ID domain_id	4ryuB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
Homologous superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

Domain ID domain_id	4ryuC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
Homologous superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

Domain ID domain_id	4ryuD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1210 — Stationary-phase Survival Protein Sure Homolog; Chain: A,
Homologous superfamily homologous superfamily	10 — Survival protein SurE-like phosphatase/nucleotidase

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Unit-cell length a length_a	160.390 Å
Unit-cell length b length_b	95.780 Å
Unit-cell length c length_c	94.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.040 Å
Low-resolution limit resolution_low	48.000 Å
R factor r_factor	0.1799
R_work r_work	0.1781
R_free r_free	0.2142

Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium

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

;5'/3'-nucleotidase SurE ;

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

4ryu__assembly_1__model_1

4ryu__assembly_1__model_1 | I(q)

4ryu__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium

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

;5'/3'-nucleotidase SurE ;

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

4ryu__assembly_1__model_1

4ryu__assembly_1__model_1 | I(q)

4ryu__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)