SAXSdb — 5v8t

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

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

Burkholderia pseudomallei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 FORMIC ACID × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A069BB90_BURPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 97–208； UniProt 2–113 Author chain B； PDBConstruct 97–208； UniProt 2–113

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

Burkholderia pseudomallei

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 FORMIC ACID × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–94； UniProt 13–97 Author chain B； PDBConstruct 10–94； UniProt 13–97

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	5v8t
Deposition date deposition_date	2017-03-22
Structure title title	Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354
Keywords keywords	Burkholderia, Peptidyl, Proline, Isomerase; ISOMERASE
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.

5v8t__assembly_1__model_1

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

Download this curve (.dat)

5v8t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5v8t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.19 Å
Rg (electron density)	18.30 Å
Total Rg	19.28 Å
Atom count	1496
Residues	191
Excluded volume	26506 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5v8t__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5v8t__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	Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
Molecular weight formula_weight	22870.6 kDa
EC 编号 ec_number	5.2.1.8
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	3202

GHHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV

Source Source

Source organism organism	Burkholderia pseudomallei
NCBI taxonomy ID ncbi_taxonomy_id	28450
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate
Molecular weight formula_weight	578.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	267

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5v8tA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5v8tB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	60.640 Å
Unit-cell length b length_b	32.500 Å
Unit-cell length c length_c	99.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	48.915 Å
R factor r_factor	0.1872
R_work r_work	0.1840
R_free r_free	0.2206

Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354

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

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

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

5v8t__assembly_1__model_1

5v8t__assembly_1__model_1 | I(q)

5v8t__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354

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

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

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

5v8t__assembly_1__model_1

5v8t__assembly_1__model_1 | I(q)

5v8t__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)