SAXSdb — 3ipp

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

Putative thiosulfate sulfurtransferase ynjE

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PHOSPHATE ION × 2 GLYCEROL × 2 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PHOSPHATE ION × 3 GLYCEROL × 1 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YNJE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–416； UniProt 20–435 Author chain B； PDBConstruct 1–416； UniProt 20–435

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	3ipp
Deposition date deposition_date	2009-08-18
Structure title title	crystal structure of sulfur-free YnjE
Keywords keywords	triple-domain rhodanese, Transferase; TRANSFERASE
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.

3ipp__assembly_1__model_1

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

Download this curve (.dat)

3ipp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ipp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.85 Å
Rg (electron density)	22.00 Å
Total Rg	22.95 Å
Atom count	3253
Residues	411
Excluded volume	57432 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ipp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ipp__assembly_2__model_1`	monomeric （1）	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 thiosulfate sulfurtransferase ynjE
Molecular weight formula_weight	46335.0 kDa
EC 编号 ec_number	2.8.1.1
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	7045

SSWAAELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKMSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAMLAKHGIRHDTTVILYGRDVYAAARVAQIMLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLMLDMEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHMEDFHNPDGTMRSADDITAMWKAWNIKPEQQVSFYCGTGWRASETFMYARAMGWKNVSVYDGGWYEWSSDPKNPVATGERGPDSSK

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21

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	5

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	431

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3ippA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	3ippA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	3ippA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	3ippB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	3ippB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	3ippB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

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Unit-cell length a length_a	160.250 Å
Unit-cell length b length_b	160.250 Å
Unit-cell length c length_c	170.821 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	46.410 Å
R factor r_factor	0.1671
R_work r_work	0.1647
R_free r_free	0.2138

crystal structure of sulfur-free YnjE

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

Putative thiosulfate sulfurtransferase ynjE

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

3ipp__assembly_1__model_1

3ipp__assembly_1__model_1 | I(q)

3ipp__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

crystal structure of sulfur-free YnjE

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

Putative thiosulfate sulfurtransferase ynjE

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

3ipp__assembly_1__model_1

3ipp__assembly_1__model_1 | I(q)

3ipp__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)